From 5aec56a2c9651df40d48605afc71656a3f77d6c1 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Johannes=20K=C3=B6ster?= Date: Thu, 18 Jul 2024 11:29:34 +0200 Subject: [PATCH 01/62] perf: update datavzrd 2.41.0 --- utils/datavzrd/environment.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/utils/datavzrd/environment.yaml b/utils/datavzrd/environment.yaml index 2ea379923c8..79ac975e436 100644 --- a/utils/datavzrd/environment.yaml +++ b/utils/datavzrd/environment.yaml @@ -2,5 +2,5 @@ channels: - conda-forge - nodefaults dependencies: - - datavzrd =2.40.0 + - datavzrd =2.41.0 - yte =1.5.4 From bb70b662c236f178dd121a4182d446521c722979 Mon Sep 17 00:00:00 2001 From: "github-actions[bot]" <41898282+github-actions[bot]@users.noreply.github.com> Date: Thu, 18 Jul 2024 11:34:38 +0200 Subject: [PATCH 02/62] chore: release 3.13.8 (#3073) :robot: I have created a release \*beep\* \*boop\* --- ### [3.13.8](https://www.github.com/snakemake/snakemake-wrappers/compare/v3.13.7...v3.13.8) (2024-07-18) ### Performance Improvements * update datavzrd 2.41.0 ([5aec56a](https://www.github.com/snakemake/snakemake-wrappers/commit/5aec56a2c9651df40d48605afc71656a3f77d6c1)) --- This PR was generated with [Release Please](https://github.com/googleapis/release-please). See [documentation](https://github.com/googleapis/release-please#release-please). Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> --- CHANGELOG.md | 7 +++++++ 1 file changed, 7 insertions(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 4c5898b7b0a..6fa9d9b996d 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -1,5 +1,12 @@ # Changelog +### [3.13.8](https://www.github.com/snakemake/snakemake-wrappers/compare/v3.13.7...v3.13.8) (2024-07-18) + + +### Performance Improvements + +* update datavzrd 2.41.0 ([5aec56a](https://www.github.com/snakemake/snakemake-wrappers/commit/5aec56a2c9651df40d48605afc71656a3f77d6c1)) + ### [3.13.7](https://www.github.com/snakemake/snakemake-wrappers/compare/v3.13.6...v3.13.7) (2024-07-12) From 9d47dd76995e4baeb2b9ea7b3278cc713e9e4f17 Mon Sep 17 00:00:00 2001 From: Felix Wiegand Date: Mon, 22 Jul 2024 16:13:53 +0200 Subject: [PATCH 03/62] perf: Update Datavzrd wrapper (#3074) ### QC * [ ] I confirm that: For all wrappers added by this PR, * there is a test case which covers any introduced changes, * `input:` and `output:` file paths in the resulting rule can be changed arbitrarily, * either the wrapper can only use a single core, or the example rule contains a `threads: x` statement with `x` being a reasonable default, * rule names in the test case are in [snake_case](https://en.wikipedia.org/wiki/Snake_case) and somehow tell what the rule is about or match the tools purpose or name (e.g., `map_reads` for a step that maps reads), * all `environment.yaml` specifications follow [the respective best practices](https://stackoverflow.com/a/64594513/2352071), * the `environment.yaml` pinning has been updated by running `snakedeploy pin-conda-envs environment.yaml` on a linux machine, * wherever possible, command line arguments are inferred and set automatically (e.g. based on file extensions in `input:` or `output:`), * all fields of the example rules in the `Snakefile`s and their entries are explained via comments (`input:`/`output:`/`params:` etc.), * `stderr` and/or `stdout` are logged correctly (`log:`), depending on the wrapped tool, * temporary files are either written to a unique hidden folder in the working directory, or (better) stored where the Python function `tempfile.gettempdir()` points to (see [here](https://docs.python.org/3/library/tempfile.html#tempfile.gettempdir); this also means that using any Python `tempfile` default behavior works), * the `meta.yaml` contains a link to the documentation of the respective tool or command, * `Snakefile`s pass the linting (`snakemake --lint`), * `Snakefile`s are formatted with [snakefmt](https://github.com/snakemake/snakefmt), * Python wrapper scripts are formatted with [black](https://black.readthedocs.io). * Conda environments use a minimal amount of channels, in recommended ordering. E.g. for bioconda, use (conda-forge, bioconda, nodefaults, as conda-forge should have highest priority and defaults channels are usually not needed because most packages are in conda-forge nowadays). --- utils/datavzrd/environment.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/utils/datavzrd/environment.yaml b/utils/datavzrd/environment.yaml index 79ac975e436..0409c9f2a0a 100644 --- a/utils/datavzrd/environment.yaml +++ b/utils/datavzrd/environment.yaml @@ -2,5 +2,5 @@ channels: - conda-forge - nodefaults dependencies: - - datavzrd =2.41.0 + - datavzrd =2.41.1 - yte =1.5.4 From 07dc08890bea0c13056d70f17a247f46c99e00ab Mon Sep 17 00:00:00 2001 From: David Laehnemann Date: Wed, 24 Jul 2024 21:29:19 +0200 Subject: [PATCH 04/62] feat: add new wrapper to create annotation tables via Ensembl biomart (#3072) ### QC * [x] I confirm that: For all wrappers added by this PR, * there is a test case which covers any introduced changes, * `input:` and `output:` file paths in the resulting rule can be changed arbitrarily, * either the wrapper can only use a single core, or the example rule contains a `threads: x` statement with `x` being a reasonable default, * rule names in the test case are in [snake_case](https://en.wikipedia.org/wiki/Snake_case) and somehow tell what the rule is about or match the tools purpose or name (e.g., `map_reads` for a step that maps reads), * all `environment.yaml` specifications follow [the respective best practices](https://stackoverflow.com/a/64594513/2352071), * the `environment.yaml` pinning has been updated by running `snakedeploy pin-conda-envs environment.yaml` on a linux machine, * wherever possible, command line arguments are inferred and set automatically (e.g. based on file extensions in `input:` or `output:`), * all fields of the example rules in the `Snakefile`s and their entries are explained via comments (`input:`/`output:`/`params:` etc.), * `stderr` and/or `stdout` are logged correctly (`log:`), depending on the wrapped tool, * temporary files are either written to a unique hidden folder in the working directory, or (better) stored where the Python function `tempfile.gettempdir()` points to (see [here](https://docs.python.org/3/library/tempfile.html#tempfile.gettempdir); this also means that using any Python `tempfile` default behavior works), * the `meta.yaml` contains a link to the documentation of the respective tool or command, * `Snakefile`s pass the linting (`snakemake --lint`), * `Snakefile`s are formatted with [snakefmt](https://github.com/snakemake/snakefmt), * Python wrapper scripts are formatted with [black](https://black.readthedocs.io). * Conda environments use a minimal amount of channels, in recommended ordering. E.g. for bioconda, use (conda-forge, bioconda, nodefaults, as conda-forge should have highest priority and defaults channels are usually not needed because most packages are in conda-forge nowadays). --- .../environment.linux-64.pin.txt | 244 ++++++++++++++++++ .../ensembl-biomart-table/environment.yaml | 8 + bio/reference/ensembl-biomart-table/meta.yaml | 41 +++ .../ensembl-biomart-table/test/Snakefile | 38 +++ bio/reference/ensembl-biomart-table/wrapper.R | 146 +++++++++++ test.py | 57 +++- 6 files changed, 531 insertions(+), 3 deletions(-) create mode 100644 bio/reference/ensembl-biomart-table/environment.linux-64.pin.txt create mode 100644 bio/reference/ensembl-biomart-table/environment.yaml create mode 100644 bio/reference/ensembl-biomart-table/meta.yaml create mode 100644 bio/reference/ensembl-biomart-table/test/Snakefile create mode 100644 bio/reference/ensembl-biomart-table/wrapper.R diff --git a/bio/reference/ensembl-biomart-table/environment.linux-64.pin.txt b/bio/reference/ensembl-biomart-table/environment.linux-64.pin.txt new file mode 100644 index 00000000000..a1d5a4bc057 --- /dev/null +++ b/bio/reference/ensembl-biomart-table/environment.linux-64.pin.txt @@ -0,0 +1,244 @@ +# This file may be used to create an environment using: +# $ conda create --name --file +# platform: linux-64 +@EXPLICIT +https://conda.anaconda.org/conda-forge/linux-64/_libgcc_mutex-0.1-conda_forge.tar.bz2#d7c89558ba9fa0495403155b64376d81 +https://conda.anaconda.org/conda-forge/noarch/_r-mutex-1.0.1-anacondar_1.tar.bz2#19f9db5f4f1b7f5ef5f6d67207f25f38 +https://conda.anaconda.org/conda-forge/noarch/_sysroot_linux-64_curr_repodata_hack-3-h69a702a_16.conda#1c005af0c6ff22814b7c52ee448d4bea +https://conda.anaconda.org/conda-forge/linux-64/ca-certificates-2024.7.4-hbcca054_0.conda#23ab7665c5f63cfb9f1f6195256daac6 +https://conda.anaconda.org/conda-forge/noarch/font-ttf-dejavu-sans-mono-2.37-hab24e00_0.tar.bz2#0c96522c6bdaed4b1566d11387caaf45 +https://conda.anaconda.org/conda-forge/noarch/font-ttf-inconsolata-3.000-h77eed37_0.tar.bz2#34893075a5c9e55cdafac56607368fc6 +https://conda.anaconda.org/conda-forge/noarch/font-ttf-source-code-pro-2.038-h77eed37_0.tar.bz2#4d59c254e01d9cde7957100457e2d5fb +https://conda.anaconda.org/conda-forge/noarch/font-ttf-ubuntu-0.83-h77eed37_2.conda#cbbe59391138ea5ad3658c76912e147f +https://conda.anaconda.org/conda-forge/linux-64/ld_impl_linux-64-2.40-hf3520f5_7.conda#b80f2f396ca2c28b8c14c437a4ed1e74 +https://conda.anaconda.org/conda-forge/noarch/libgcc-devel_linux-64-14.1.0-h5d3d1c9_100.conda#6d4f65dc440f7b3422113b135be19703 +https://conda.anaconda.org/conda-forge/noarch/libstdcxx-devel_linux-64-14.1.0-h5d3d1c9_100.conda#cedc62fd8c4cf28f23d3cd5db7839e99 +https://conda.anaconda.org/conda-forge/linux-64/pandoc-3.2.1-ha770c72_0.conda#b39b12d3809e4042f832b76192e0e7e8 +https://conda.anaconda.org/conda-forge/linux-64/python_abi-3.12-4_cp312.conda#dccc2d142812964fcc6abdc97b672dff +https://conda.anaconda.org/conda-forge/noarch/tzdata-2024a-h0c530f3_0.conda#161081fc7cec0bfda0d86d7cb595f8d8 +https://conda.anaconda.org/conda-forge/noarch/fonts-conda-forge-1-0.tar.bz2#f766549260d6815b0c52253f1fb1bb29 +https://conda.anaconda.org/conda-forge/noarch/kernel-headers_linux-64-3.10.0-h4a8ded7_16.conda#ff7f38675b226cfb855aebfc32a13e31 +https://conda.anaconda.org/conda-forge/linux-64/libgomp-14.1.0-h77fa898_0.conda#ae061a5ed5f05818acdf9adab72c146d +https://conda.anaconda.org/conda-forge/linux-64/_openmp_mutex-4.5-2_gnu.tar.bz2#73aaf86a425cc6e73fcf236a5a46396d +https://conda.anaconda.org/conda-forge/noarch/fonts-conda-ecosystem-1-0.tar.bz2#fee5683a3f04bd15cbd8318b096a27ab +https://conda.anaconda.org/conda-forge/noarch/sysroot_linux-64-2.17-h4a8ded7_16.conda#223fe8a3ff6d5e78484a9d58eb34d055 +https://conda.anaconda.org/conda-forge/linux-64/binutils_impl_linux-64-2.40-ha1999f0_7.conda#3f840c7ed70a96b5ebde8044b2f36f32 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+https://conda.anaconda.org/conda-forge/noarch/r-modelr-0.1.11-r43hc72bb7e_2.conda#2cdd8c74b0c949695af0debfd3a44974 +https://conda.anaconda.org/bioconda/noarch/bioconductor-biomart-2.58.0-r43hdfd78af_0.tar.bz2#863f49a8729f533415ec09e562fa7f3c +https://conda.anaconda.org/conda-forge/noarch/r-tidyverse-2.0.0-r43h785f33e_1.conda#390310ae8a44cbd35c8d27f5efa362cb diff --git a/bio/reference/ensembl-biomart-table/environment.yaml b/bio/reference/ensembl-biomart-table/environment.yaml new file mode 100644 index 00000000000..bc05f445260 --- /dev/null +++ b/bio/reference/ensembl-biomart-table/environment.yaml @@ -0,0 +1,8 @@ +channels: + - conda-forge + - bioconda + - nodefaults +dependencies: + - bioconductor-biomart =2.58 + - r-nanoparquet =0.3 + - r-tidyverse = 2.0 \ No newline at end of file diff --git a/bio/reference/ensembl-biomart-table/meta.yaml b/bio/reference/ensembl-biomart-table/meta.yaml new file mode 100644 index 00000000000..18e7887597c --- /dev/null +++ b/bio/reference/ensembl-biomart-table/meta.yaml @@ -0,0 +1,41 @@ +name: ensembl-biomart-table +description: > + Create a table of annotations available via the ``bioconductor-biomart``, + with one column per specified annotation (for example ``ensembl_gene_id``, + ``ensembl_transcript_id``, ``ext_gene``, ... for the human reference). For + reference, have a look at the + `Ensembl biomart online `_ + or at the ``biomaRt`` package documentation linked in the ``URL`` field. +url: https://bioconductor.org/packages/deveol/bioc/vignettes/biomaRt/inst/doc/accessing_ensembl.html +authors: + - David Lähnemann +output: + - > + tab-separated values (``.tsv``); for supported compression extensions, see + `the write_tsv documentation page `_ + - > + parquet (``.parquet``) file; for supported compression algorithms, see + `the write_parquet documentation page `_ +params: + - biomart: > + for example, 'genes'; for options, see + `the documentation on identifying databases `_ + - species: > + species that has a 'genes' database / dataset available via the Ensembl + BioMart (for example, 'homo_sapiens'), for example check the + `Ensembl species list `_ + - build: build available for the selected species, for example 'GRCh38' + - release: release from which the species and build are available, for example '112' + - attributes: > + A list of wanted annotation columns ("database attributes"). For + finding available attributes, see the + `instructions in the biomaRt documentation `_. + Note that these need to be available for the combination of species, + build and release from the specified biomart database. + - filters: > + (optional) This will restrict the download and output to the filters you + specify. The format is a dictionary, for example + ``{"chromosome_name": ["X", "Y"]}``. Note that non-existing filter values + (for example a ``chromosomes_name`` of ``"Z"``) will simply be ignored + without error or warning. For finding available filters, see the + `instructions in the biomaRt documentation `_. \ No newline at end of file diff --git a/bio/reference/ensembl-biomart-table/test/Snakefile b/bio/reference/ensembl-biomart-table/test/Snakefile new file mode 100644 index 00000000000..9e2113c2577 --- /dev/null +++ b/bio/reference/ensembl-biomart-table/test/Snakefile @@ -0,0 +1,38 @@ +rule create_transcripts_to_genes_mapping: + output: + table="resources/ensembl_transcripts_to_genes_mapping.tsv.gz", # .gz extension is optional, but recommended + params: + biomart="genes", + species="homo_sapiens", + build="GRCh38", + release="112", + attributes=[ + "ensembl_transcript_id", + "ensembl_gene_id", + "external_gene_name", + "genecards", + "chromosome_name", + ], + filters={ "chromosome_name": ["22", "X"] }, # optional: restrict output by using filters + log: + "logs/create_transcripts_to_genes_mapping.log", + cache: "omit-software" # save space and time with between workflow caching (see docs) + wrapper: + "master/bio/reference/ensembl-biomart-table" + + +rule create_transcripts_to_genes_mapping_parquet: + output: + table="resources/ensembl_transcripts_to_genes_mapping.parquet.gz", # .gz extension is optional, but recommended + params: + biomart="genes", + species="mus_musculus", + build="GRCm39", + release="112", + attributes=["ensembl_transcript_id", "ensembl_gene_id"], + # filters={ "chromosome_name": "19"}, # optional: restrict output by using filters + log: + "logs/create_transcripts_to_genes_mapping_parquet.log", + cache: "omit-software" # save space and time with between workflow caching (see docs) + wrapper: + "master/bio/reference/ensembl-biomart-table" diff --git a/bio/reference/ensembl-biomart-table/wrapper.R b/bio/reference/ensembl-biomart-table/wrapper.R new file mode 100644 index 00000000000..1ad9450c701 --- /dev/null +++ b/bio/reference/ensembl-biomart-table/wrapper.R @@ -0,0 +1,146 @@ +# __author__ = "David Lähnemann" +# __copyright__ = "Copyright 2024, David Lähnemann" +# __email__ = "david.laehnemann@hhu.de" +# __license__ = "MIT" + +log <- file(snakemake@log[[1]], open="wt") +sink(log) +sink(log, type="message") + +library("tidyverse") +library("nanoparquet") +rlang::global_entrace() +library("fs") +library("cli") + +library("biomaRt") + +wanted_biomart <- snakemake@params[["biomart"]] +# bioconductor-biomart needs the species as something like `hsapiens` instead +# of `homo_sapiens`, and `chyarkandensis` instead of `cervus_hanglu_yarkandensis` +species_name_components <- str_split(snakemake@params[["species"]], "_")[[1]] +if (length(species_name_components) == 2) { + wanted_species <- str_c( + str_sub(species_name_components[1], 1, 1), + species_name_components[2] + ) +} else if (length(species_name_components) == 3) { + wanted_species <- str_c( + str_sub(species_name_components[1], 1, 1), + str_sub(species_name_components[2], 1, 1), + species_name_components[3] + ) +} else { + cli_abort(c( + "Unsupported species name '{snakemake@params[['species']]}'.", + "x" = "Splitting on underscores led to unexpected number of name components: {length(species_name_components)}.", + "i" = "Expected species name with 2 (e.g. `homo_sapiens`) or 3 (e.g. `cervus_hanglu_yarkandensis`) components.", + "Anything else either does not exist in Ensembl, or we don't yet handle it properly.", + "In case you are sure the species you specified is correct and exists in Ensembl, please", + "file a bug report as an issue on GitHub, referencing this file: ", + "https://github.com/snakemake/snakemake-wrappers/blob/master/bio/reference/ensembl-biomart-table/wrapper.R" + )) +} + +wanted_release <- snakemake@params[["release"]] +wanted_build <- snakemake@params[["build"]] + +wanted_filters <- snakemake@params[["filters"]] + +wanted_columns <- snakemake@params[["attributes"]] + +output_filename <- snakemake@output[["table"]] + +if (wanted_build == "GRCh37") { + grch <- "37" + version <- NULL + cli_warn(c( + "As you specified build 'GRCH37' in your configuration yaml, biomart forces", + "us to ignore the release you specified ('{release}')." + )) +} else { + grch <- NULL + version <- wanted_release +} + +get_mart <- function(biomart, species, build, version, grch, dataset) { + mart <- useEnsembl( + biomart = biomart, + dataset = str_c(species, "_", dataset), + version = version, + GRCh = grch + ) + + if (build == "GRCh37") { + retrieved_build <- str_remove(listDatasets(mart)$version, "\\..*") + } else { + retrieved_build <- str_remove(searchDatasets(mart, species)$version, "\\..*") + } + + if (retrieved_build != build) { + cli_abort(c( + "The Ensembl release and genome build number you specified are not compatible.", + "x" = "Genome build '{build}' not available via biomart for Ensembl release '{release}'.", + "i" = "Ensembl release '{release}' only provides build '{retrieved_build}'.", + " " = "Please fix your configuration yaml file's reference entry, you have two options:", + "*" = "Change the build entry to '{retrieved_build}'.", + "*" = "Change the release entry to one that provides build '{build}'. You have to determine this from biomart by yourself." + )) + } + mart +} + +gene_ensembl <- get_mart(wanted_biomart, wanted_species, wanted_build, version, grch, "gene_ensembl") + +if ( !is.null(wanted_filters) ) { + table <- getBM( + attributes = wanted_columns, + filters = names(wanted_filters), + values = unname(wanted_filters), + mart = gene_ensembl + ) |> as_tibble() +} else { + table <- getBM( + attributes = wanted_columns, + mart = gene_ensembl + ) |> as_tibble() +} + + + +if ( str_detect(output_filename, "tsv(\\.(gz|bz2|xz))?$") ) { + write_tsv( + x = table, + file = output_filename + ) +} else if ( str_detect(output_filename, "\\.parquet") ) { + last_ext <- path_ext(output_filename) + compression <- case_match( + last_ext, + "parquet" ~ "uncompressed", + "gz" ~ "gzip", + "zst" ~ "zstd", + "sz" ~ "snappy" + ) + if ( is.na(compression) ) { + cli_abort( + "File extension '{last_ext}' not supported for writing with the used nanoparquet version.", + "x" = "Cannot write to a file '{output_filename}', because the version of the package", + "nanoparquet used does not support writing files of type '{last_ext}'.", + "i" = "For supported file types, see: https://r-lib.github.io/nanoparquet/reference/write_parquet.html" + ) + } + write_parquet( + x = table, + file = output_filename, + compression = compression + ) +} else { + cli_abort(c( + "Unsupported file format in output file '{output_filename}'.", + "x" = "Only '.tsv' and '.parquet' files are supported, with certain compression variants each.", + "i" = "For supported compression extensions, see:", + "*" = "tsv: https://readr.tidyverse.org/reference/write_delim.html#output", + "*" = "parquet: https://r-lib.github.io/nanoparquet/reference/write_parquet.html#arguments" + )) +} diff --git a/test.py b/test.py index 35aadbd6172..11b81bd6db3 100644 --- a/test.py +++ b/test.py @@ -5602,7 +5602,14 @@ def test_ensembl_annotation_gtf_gz(): def test_ensembl_regulatory_gff3_gz(): run( "bio/reference/ensembl-regulation", - ["snakemake", "--cores", "1", "resources/regulatory_features.gff3.gz", "--use-conda", "-F"], + [ + "snakemake", + "--cores", + "1", + "resources/regulatory_features.gff3.gz", + "--use-conda", + "-F", + ], ) @@ -5610,7 +5617,14 @@ def test_ensembl_regulatory_gff3_gz(): def test_ensembl_regulatory_features_grch37_gff(): run( "bio/reference/ensembl-regulation", - ["snakemake", "--cores", "1", "resources/regulatory_features.gff", "--use-conda", "-F"], + [ + "snakemake", + "--cores", + "1", + "resources/regulatory_features.gff", + "--use-conda", + "-F", + ], ) @@ -5618,7 +5632,44 @@ def test_ensembl_regulatory_features_grch37_gff(): def test_ensembl_regulatory_features_mouse_gff_gz(): run( "bio/reference/ensembl-regulation", - ["snakemake", "--cores", "1", "resources/regulatory_features.mouse.gff.gz", "--use-conda", "-F"], + [ + "snakemake", + "--cores", + "1", + "resources/regulatory_features.mouse.gff.gz", + "--use-conda", + "-F", + ], + ) + + +@skip_if_not_modified +def test_ensembl_transcripts_to_genes_mapping(): + run( + "bio/reference/ensembl-biomart-table", + [ + "snakemake", + "--cores", + "1", + "resources/ensembl_transcripts_to_genes_mapping.tsv.gz", + "--use-conda", + "-F", + ], + ) + + +@skip_if_not_modified +def test_ensembl_transcripts_to_genes_mapping_parquet(): + run( + "bio/reference/ensembl-biomart-table", + [ + "snakemake", + "--cores", + "1", + "resources/ensembl_transcripts_to_genes_mapping.parquet.gz", + "--use-conda", + "-F", + ], ) From 86ec8769ddb9a881ca28d0b4600e24b5f9d41229 Mon Sep 17 00:00:00 2001 From: "snakedeploy-bot[bot]" <115615832+snakedeploy-bot[bot]@users.noreply.github.com> Date: Fri, 26 Jul 2024 01:40:16 +0000 Subject: [PATCH 05/62] perf: autobump bio/blast/makeblastdb (#3078) Automatic bump of bio/blast/makeblastdb. --------- Co-authored-by: snakedeploy-bot[bot] <115615832+snakedeploy-bot[bot]@users.noreply.github.com> --- .../makeblastdb/environment.linux-64.pin.txt | 89 +++++++------------ bio/blast/makeblastdb/environment.yaml | 2 +- 2 files changed, 33 insertions(+), 58 deletions(-) diff --git a/bio/blast/makeblastdb/environment.linux-64.pin.txt b/bio/blast/makeblastdb/environment.linux-64.pin.txt index aaf65944f9d..d541457b488 100644 --- a/bio/blast/makeblastdb/environment.linux-64.pin.txt +++ b/bio/blast/makeblastdb/environment.linux-64.pin.txt @@ -3,84 +3,59 @@ # platform: linux-64 @EXPLICIT https://conda.anaconda.org/conda-forge/linux-64/_libgcc_mutex-0.1-conda_forge.tar.bz2#d7c89558ba9fa0495403155b64376d81 -https://conda.anaconda.org/conda-forge/linux-64/ca-certificates-2023.7.22-hbcca054_0.conda#a73ecd2988327ad4c8f2c331482917f2 -https://conda.anaconda.org/conda-forge/linux-64/libstdcxx-ng-13.2.0-h7e041cc_3.conda#937eaed008f6bf2191c5fe76f87755e9 -https://conda.anaconda.org/conda-forge/linux-64/libgomp-13.2.0-h807b86a_3.conda#7124cbb46b13d395bdde68f2d215c989 +https://conda.anaconda.org/conda-forge/linux-64/ca-certificates-2024.7.4-hbcca054_0.conda#23ab7665c5f63cfb9f1f6195256daac6 +https://conda.anaconda.org/conda-forge/linux-64/libgomp-14.1.0-h77fa898_0.conda#ae061a5ed5f05818acdf9adab72c146d https://conda.anaconda.org/conda-forge/linux-64/_openmp_mutex-4.5-2_gnu.tar.bz2#73aaf86a425cc6e73fcf236a5a46396d -https://conda.anaconda.org/conda-forge/linux-64/libgcc-ng-13.2.0-h807b86a_3.conda#23fdf1fef05baeb7eadc2aed5fb0011f -https://conda.anaconda.org/conda-forge/linux-64/bzip2-1.0.8-hd590300_5.conda#69b8b6202a07720f448be700e300ccf4 -https://conda.anaconda.org/conda-forge/linux-64/c-ares-1.21.0-hd590300_0.conda#c06fa0440048270817b9e3142cc661bf -https://conda.anaconda.org/conda-forge/linux-64/gettext-0.21.1-h27087fc_0.tar.bz2#14947d8770185e5153fdd04d4673ed37 -https://conda.anaconda.org/conda-forge/linux-64/icu-70.1-h27087fc_0.tar.bz2#87473a15119779e021c314249d4b4aed +https://conda.anaconda.org/conda-forge/linux-64/libgcc-ng-14.1.0-h77fa898_0.conda#ca0fad6a41ddaef54a153b78eccb5037 +https://conda.anaconda.org/conda-forge/linux-64/bzip2-1.0.8-h4bc722e_7.conda#62ee74e96c5ebb0af99386de58cf9553 +https://conda.anaconda.org/conda-forge/linux-64/c-ares-1.32.3-h4bc722e_0.conda#7624e34ee6baebfc80d67bac76cc9d9d +https://conda.anaconda.org/conda-forge/linux-64/gettext-tools-0.22.5-h59595ed_2.conda#985f2f453fb72408d6b6f1be0f324033 https://conda.anaconda.org/conda-forge/linux-64/keyutils-1.6.1-h166bdaf_0.tar.bz2#30186d27e2c9fa62b45fb1476b7200e3 -https://conda.anaconda.org/conda-forge/linux-64/libev-4.33-h516909a_1.tar.bz2#6f8720dff19e17ce5d48cfe7f3d2f0a3 -https://conda.anaconda.org/conda-forge/linux-64/libiconv-1.17-h166bdaf_0.tar.bz2#b62b52da46c39ee2bc3c162ac7f1804d -https://conda.anaconda.org/conda-forge/linux-64/libnsl-2.0.1-hd590300_0.conda#30fd6e37fe21f86f4bd26d6ee73eeec7 +https://conda.anaconda.org/conda-forge/linux-64/libev-4.33-hd590300_2.conda#172bf1cd1ff8629f2b1179945ed45055 +https://conda.anaconda.org/conda-forge/linux-64/libgettextpo-0.22.5-h59595ed_2.conda#172bcc51059416e7ce99e7b528cede83 +https://conda.anaconda.org/conda-forge/linux-64/libstdcxx-ng-14.1.0-hc0a3c3a_0.conda#1cb187a157136398ddbaae90713e2498 https://conda.anaconda.org/conda-forge/linux-64/libunistring-0.9.10-h7f98852_0.tar.bz2#7245a044b4a1980ed83196176b78b73a -https://conda.anaconda.org/conda-forge/linux-64/libzlib-1.2.13-hd590300_5.conda#f36c115f1ee199da648e0597ec2047ad -https://conda.anaconda.org/conda-forge/linux-64/ncurses-6.4-h59595ed_2.conda#7dbaa197d7ba6032caf7ae7f32c1efa0 -https://conda.anaconda.org/conda-forge/linux-64/openssl-3.1.4-hd590300_0.conda#412ba6938c3e2abaca8b1129ea82e238 -https://conda.anaconda.org/conda-forge/linux-64/ossuuid-1.6.2-hf484d3e_1000.tar.bz2#0ca24876ead80a9290d3936aea5fefb1 -https://conda.anaconda.org/conda-forge/linux-64/pcre-8.45-h9c3ff4c_0.tar.bz2#c05d1820a6d34ff07aaaab7a9b7eddaa -https://conda.anaconda.org/conda-forge/linux-64/xz-5.2.6-h166bdaf_0.tar.bz2#2161070d867d1b1204ea749c8eec4ef0 +https://conda.anaconda.org/conda-forge/linux-64/libxcrypt-4.4.36-hd590300_1.conda#5aa797f8787fe7a17d1b0821485b5adc +https://conda.anaconda.org/conda-forge/linux-64/libzlib-1.3.1-h4ab18f5_1.conda#57d7dc60e9325e3de37ff8dffd18e814 +https://conda.anaconda.org/conda-forge/linux-64/ncurses-6.5-h59595ed_0.conda#fcea371545eda051b6deafb24889fc69 +https://conda.anaconda.org/conda-forge/linux-64/openssl-3.3.1-h4bc722e_2.conda#e1b454497f9f7c1147fdde4b53f1b512 +https://conda.anaconda.org/conda-forge/linux-64/libasprintf-0.22.5-h661eb56_2.conda#dd197c968bf9760bba0031888d431ede https://conda.anaconda.org/conda-forge/linux-64/libedit-3.1.20191231-he28a2e2_2.tar.bz2#4d331e44109e3f0e19b4cb8f9b82f3e1 -https://conda.anaconda.org/conda-forge/linux-64/libidn2-2.3.4-h166bdaf_0.tar.bz2#7440fbafd870b8bab68f83a064875d34 -https://conda.anaconda.org/conda-forge/linux-64/libnghttp2-1.58.0-h47da74e_0.conda#9b13d5ee90fc9f09d54fd403247342b4 -https://conda.anaconda.org/conda-forge/linux-64/libsqlite-3.44.0-h2797004_0.conda#b58e6816d137f3aabf77d341dd5d732b +https://conda.anaconda.org/conda-forge/linux-64/libgettextpo-devel-0.22.5-h59595ed_2.conda#b63d9b6da3653179a278077f0de20014 +https://conda.anaconda.org/conda-forge/linux-64/libnghttp2-1.58.0-h47da74e_1.conda#700ac6ea6d53d5510591c4344d5c989a +https://conda.anaconda.org/conda-forge/linux-64/libsqlite-3.46.0-hde9e2c9_0.conda#18aa975d2094c34aef978060ae7da7d8 https://conda.anaconda.org/conda-forge/linux-64/libssh2-1.11.0-h0841786_0.conda#1f5a58e686b13bcfde88b93f547d23fe -https://conda.anaconda.org/conda-forge/linux-64/libxml2-2.9.14-h22db469_4.tar.bz2#aced7c1f4b4dbfea08e033c6ae97c53e -https://conda.anaconda.org/conda-forge/linux-64/perl-5.32.1-4_hd590300_perl5.conda#3e785bff761095eb7f8676f4694bd1b1 -https://conda.anaconda.org/conda-forge/linux-64/zlib-1.2.13-hd590300_5.conda#68c34ec6149623be41a1933ab996a209 -https://conda.anaconda.org/conda-forge/linux-64/zstd-1.5.5-hfc55251_0.conda#04b88013080254850d6c01ed54810589 -https://conda.anaconda.org/conda-forge/linux-64/krb5-1.21.2-h659d440_0.conda#cd95826dbd331ed1be26bdf401432844 -https://conda.anaconda.org/conda-forge/linux-64/perl-capture-tiny-0.48-pl5321ha770c72_1.tar.bz2#4859b3d284090166394875e68184dc9c +https://conda.anaconda.org/bioconda/linux-64/ncbi-vdb-3.1.1-h4ac6f70_1.tar.bz2#05705db906896430d0d963de7a3c1698 +https://conda.anaconda.org/conda-forge/linux-64/pcre-8.45-h9c3ff4c_0.tar.bz2#c05d1820a6d34ff07aaaab7a9b7eddaa +https://conda.anaconda.org/conda-forge/linux-64/perl-5.32.1-7_hd590300_perl5.conda#f2cfec9406850991f4e3d960cc9e3321 +https://conda.anaconda.org/conda-forge/linux-64/zlib-1.3.1-h4ab18f5_1.conda#9653f1bf3766164d0e65fa723cabbc54 +https://conda.anaconda.org/conda-forge/linux-64/zstd-1.5.6-ha6fb4c9_0.conda#4d056880988120e29d75bfff282e0f45 +https://conda.anaconda.org/conda-forge/linux-64/krb5-1.21.3-h659f571_0.conda#3f43953b7d3fb3aaa1d0d0723d91e368 +https://conda.anaconda.org/conda-forge/linux-64/libasprintf-devel-0.22.5-h661eb56_2.conda#02e41ab5834dcdcc8590cf29d9526f50 https://conda.anaconda.org/conda-forge/noarch/perl-common-sense-3.75-pl5321hd8ed1ab_0.tar.bz2#ef70dc77e8b10bbb62f5e843b401ef0e https://conda.anaconda.org/conda-forge/linux-64/perl-compress-raw-bzip2-2.201-pl5321h166bdaf_0.tar.bz2#105e211458bf45fe64b6de5ae8283ba4 https://conda.anaconda.org/conda-forge/linux-64/perl-compress-raw-zlib-2.202-pl5321h166bdaf_0.tar.bz2#66176366c49e2f70b3a764bc744b5010 -https://conda.anaconda.org/conda-forge/noarch/perl-constant-1.33-pl5321hd8ed1ab_0.tar.bz2#7f9fc9cfa08a3fe36ffcff820c65c3ac https://conda.anaconda.org/conda-forge/noarch/perl-exporter-5.74-pl5321hd8ed1ab_0.tar.bz2#fd2eac4e35f8c970870a3961c1df3e29 https://conda.anaconda.org/conda-forge/noarch/perl-exporter-tiny-1.002002-pl5321hd8ed1ab_0.tar.bz2#48d709826875be1f2c108d3d1d8efec7 https://conda.anaconda.org/conda-forge/noarch/perl-extutils-makemaker-7.70-pl5321hd8ed1ab_0.conda#ec3e57ed34f7765bfc7054a05868ce5d -https://conda.anaconda.org/bioconda/noarch/perl-ffi-checklib-0.28-pl5321hdfd78af_0.tar.bz2#05451eeb5e82ccf46831248c55c6218a -https://conda.anaconda.org/conda-forge/noarch/perl-file-which-1.24-pl5321hd8ed1ab_0.tar.bz2#94e5b2c9d56ef7c4c70ddf51ac38ae3d -https://conda.anaconda.org/conda-forge/noarch/perl-importer-0.026-pl5321hd8ed1ab_0.tar.bz2#66e17c342d13c39a12c1059f13f9b72c https://conda.anaconda.org/bioconda/noarch/perl-io-zlib-1.14-pl5321hdfd78af_0.tar.bz2#eadd0d684a0e22f08cccd6783c97606e https://conda.anaconda.org/bioconda/linux-64/perl-list-moreutils-xs-0.430-pl5321h031d066_2.tar.bz2#116a0e93733b7004356aef80a1751dec https://conda.anaconda.org/conda-forge/noarch/perl-parent-0.241-pl5321hd8ed1ab_0.conda#44ab631ed23c25c224ed4c849d713aac -https://conda.anaconda.org/conda-forge/noarch/perl-path-tiny-0.124-pl5321hd8ed1ab_0.tar.bz2#456a8757a2e5272fb1dcb6435e037f3a https://conda.anaconda.org/conda-forge/linux-64/perl-scalar-list-utils-1.63-pl5321h166bdaf_0.tar.bz2#c8d96f52c1e8de80663f2e11fbabfd0d -https://conda.anaconda.org/conda-forge/noarch/perl-scope-guard-0.21-pl5321hd8ed1ab_0.tar.bz2#daea4e61dfdf06fef9a51dce492508f4 https://conda.anaconda.org/conda-forge/linux-64/perl-storable-3.15-pl5321h166bdaf_0.tar.bz2#1e9fb913a11eb8a17d6556efbea1e13d -https://conda.anaconda.org/conda-forge/linux-64/perl-test-warnings-0.031-pl5321ha770c72_0.conda#db0eb51272ea7af7213afaaf7e9967c3 -https://conda.anaconda.org/conda-forge/linux-64/perl-try-tiny-0.31-pl5321ha770c72_0.tar.bz2#cc23b14ed56bf51d84832d98ebd156af -https://conda.anaconda.org/conda-forge/noarch/perl-xml-sax-base-1.09-pl5321hd8ed1ab_0.tar.bz2#a4d9b02cd61c478c9cb58064307a1414 -https://conda.anaconda.org/conda-forge/linux-64/wget-1.20.3-ha35d2d1_1.tar.bz2#c990e108f39e1b43adf61e984360c9a1 -https://conda.anaconda.org/bioconda/linux-64/entrez-direct-16.2-he881be0_1.tar.bz2#ff30142050ba583481215a6e1b3a5de0 -https://conda.anaconda.org/conda-forge/linux-64/libcurl-8.4.0-hca28451_0.conda#1158ac1d2613b28685644931f11ee807 +https://conda.anaconda.org/conda-forge/linux-64/gettext-0.22.5-h59595ed_2.conda#219ba82e95d7614cf7140d2a4afc0926 +https://conda.anaconda.org/conda-forge/linux-64/libcurl-8.9.0-hdb1bdb2_0.conda#5badfbdb2688d8aaca7bd3c98d557b97 https://conda.anaconda.org/conda-forge/noarch/perl-carp-1.50-pl5321hd8ed1ab_0.tar.bz2#bdddc03e28019b902da71b722f2288d7 -https://conda.anaconda.org/conda-forge/linux-64/perl-encode-3.19-pl5321h166bdaf_0.tar.bz2#ee3502fa957b5c53071c5d7c7ee62f59 -https://conda.anaconda.org/conda-forge/noarch/perl-file-path-2.18-pl5321hd8ed1ab_0.tar.bz2#e13e456f61b8261ba074c0aa93086afe +https://conda.anaconda.org/conda-forge/linux-64/perl-encode-3.21-pl5321hd590300_0.conda#704fb52dc57c97cf5adcc057c8b40a0a https://conda.anaconda.org/bioconda/noarch/perl-list-moreutils-0.430-pl5321hdfd78af_0.tar.bz2#7f04c79d216d0f8e7b6d5a51de4aafa0 -https://conda.anaconda.org/conda-forge/linux-64/perl-test-fatal-0.016-pl5321ha770c72_0.tar.bz2#5c397b1fd3095004f4ff149af1c0dd3c https://conda.anaconda.org/bioconda/noarch/perl-types-serialiser-1.01-pl5321hdfd78af_0.tar.bz2#cfc65753e827bbef80c00eaa395f6ae7 -https://conda.anaconda.org/conda-forge/noarch/perl-xml-namespacesupport-1.12-pl5321hd8ed1ab_0.tar.bz2#f4ce684ba66b3228bfffb09892235930 -https://conda.anaconda.org/conda-forge/linux-64/curl-8.4.0-hca28451_0.conda#2bcf7689cae931dd35d9a45626f49fce -https://conda.anaconda.org/conda-forge/noarch/perl-business-isbn-data-20210112.006-pl5321hd8ed1ab_0.tar.bz2#a70f08650ec3919ee5e599834f1349d3 -https://conda.anaconda.org/conda-forge/noarch/perl-file-temp-0.2304-pl5321hd8ed1ab_0.tar.bz2#0a039c4fc36748942287ee10d0431515 +https://conda.anaconda.org/conda-forge/linux-64/curl-8.9.0-h18eb788_0.conda#cb385c8a955ad49c3342b23cd1a26c11 +https://conda.anaconda.org/conda-forge/linux-64/libidn2-2.3.7-hd590300_0.conda#2b7b0d827c6447cc1d85dc06d5b5de46 https://conda.anaconda.org/bioconda/linux-64/perl-io-compress-2.201-pl5321hdbdd923_2.tar.bz2#f40f599ce37ad75715bab686baa08197 https://conda.anaconda.org/bioconda/linux-64/perl-json-xs-2.34-pl5321h4ac6f70_6.tar.bz2#e01a73e25a790b129920f9e663e4935f https://conda.anaconda.org/conda-forge/linux-64/perl-pathtools-3.75-pl5321h166bdaf_0.tar.bz2#4e72abd06ec15cb28c14798dab2c10c8 -https://conda.anaconda.org/conda-forge/noarch/perl-sub-info-0.002-pl5321hd8ed1ab_0.tar.bz2#5b48dcf7df9e4e01d45de2c1f494d830 -https://conda.anaconda.org/bioconda/noarch/perl-term-table-0.016-pl5321hdfd78af_0.tar.bz2#91a4c19686c0e1c8b34325664bd3eee4 https://conda.anaconda.org/bioconda/noarch/perl-archive-tar-2.40-pl5321hdfd78af_0.tar.bz2#ef5f007762b5ad9425694104d7db4463 -https://conda.anaconda.org/conda-forge/noarch/perl-business-isbn-3.007-pl5321hd8ed1ab_0.tar.bz2#a7a3d7614e1a73b8d9c20030651d6006 -https://conda.anaconda.org/conda-forge/noarch/perl-file-chdir-0.1011-pl5321hd8ed1ab_0.tar.bz2#c057570093f9298e9c5e4391877f2301 https://conda.anaconda.org/bioconda/noarch/perl-json-4.10-pl5321hdfd78af_0.tar.bz2#05467eeb1e57206d8dddf31c3128cd00 -https://conda.anaconda.org/bioconda/noarch/perl-test2-suite-0.000145-pl5321hdfd78af_0.tar.bz2#c07db9debdb82d45be8a2115f5eb952d -https://conda.anaconda.org/conda-forge/noarch/perl-xml-sax-1.02-pl5321hd8ed1ab_0.tar.bz2#3e3fac6ffef3fcda271b5511aecacaa8 -https://conda.anaconda.org/bioconda/linux-64/perl-alien-build-2.48-pl5321hec16e2b_0.tar.bz2#8b1ea03a11ce6b27945962c47013f93e -https://conda.anaconda.org/conda-forge/linux-64/perl-uri-5.17-pl5321ha770c72_0.conda#847c007d5f4a59b356a9cd577010b89c -https://conda.anaconda.org/bioconda/linux-64/perl-alien-libxml2-0.17-pl5321hec16e2b_0.tar.bz2#4628ba7447031d6e4661732a2e7bdc64 -https://conda.anaconda.org/bioconda/linux-64/perl-xml-libxml-2.0207-pl5321h661654b_0.tar.bz2#1ce8ba66c656dbe547110201b1456797 -https://conda.anaconda.org/bioconda/linux-64/ncbi-vdb-3.0.8-hdbdd923_0.tar.bz2#3b58cf2b702f96d812c67466456fe251 -https://conda.anaconda.org/bioconda/linux-64/blast-2.15.0-pl5321h6f7f691_1.tar.bz2#f7e6a87317b5d00469d39a2d1ef2698f +https://conda.anaconda.org/conda-forge/linux-64/wget-1.21.4-hda4d442_0.conda#361e96b664eac64a33c20dfd11affbff +https://conda.anaconda.org/bioconda/linux-64/entrez-direct-22.4-he881be0_0.tar.bz2#0994f567f11543b7aea1afce884c2ce6 +https://conda.anaconda.org/bioconda/linux-64/blast-2.16.0-h6f7f691_0.tar.bz2#098092890e9c94de10a3fe827339bc16 diff --git a/bio/blast/makeblastdb/environment.yaml b/bio/blast/makeblastdb/environment.yaml index d6a2cb7075f..97060d39ce6 100644 --- a/bio/blast/makeblastdb/environment.yaml +++ b/bio/blast/makeblastdb/environment.yaml @@ -3,4 +3,4 @@ channels: - bioconda - nodefaults dependencies: - - blast =2.15.0 + - blast =2.16.0 From 01dc16fdebfab3ee6f36983a317fc8ea731f1d44 Mon Sep 17 00:00:00 2001 From: "snakedeploy-bot[bot]" <115615832+snakedeploy-bot[bot]@users.noreply.github.com> Date: Fri, 26 Jul 2024 01:45:11 +0000 Subject: [PATCH 06/62] perf: autobump bio/bwa/mem (#3079) Automatic bump of bio/bwa/mem. --------- Co-authored-by: snakedeploy-bot[bot] <115615832+snakedeploy-bot[bot]@users.noreply.github.com> --- bio/bwa/mem/environment.linux-64.pin.txt | 52 ++++++++++++------------ bio/bwa/mem/environment.yaml | 2 +- 2 files changed, 27 insertions(+), 27 deletions(-) diff --git a/bio/bwa/mem/environment.linux-64.pin.txt b/bio/bwa/mem/environment.linux-64.pin.txt index 76594ed00a7..e1713699f58 100644 --- a/bio/bwa/mem/environment.linux-64.pin.txt +++ b/bio/bwa/mem/environment.linux-64.pin.txt @@ -3,7 +3,7 @@ # platform: linux-64 @EXPLICIT https://conda.anaconda.org/conda-forge/linux-64/_libgcc_mutex-0.1-conda_forge.tar.bz2#d7c89558ba9fa0495403155b64376d81 -https://conda.anaconda.org/conda-forge/linux-64/ca-certificates-2024.6.2-hbcca054_0.conda#847c3c2905cc467cea52c24f9cfa8080 +https://conda.anaconda.org/conda-forge/linux-64/ca-certificates-2024.7.4-hbcca054_0.conda#23ab7665c5f63cfb9f1f6195256daac6 https://conda.anaconda.org/conda-forge/noarch/font-ttf-dejavu-sans-mono-2.37-hab24e00_0.tar.bz2#0c96522c6bdaed4b1566d11387caaf45 https://conda.anaconda.org/conda-forge/noarch/font-ttf-inconsolata-3.000-h77eed37_0.tar.bz2#34893075a5c9e55cdafac56607368fc6 https://conda.anaconda.org/conda-forge/noarch/font-ttf-source-code-pro-2.038-h77eed37_0.tar.bz2#4d59c254e01d9cde7957100457e2d5fb @@ -11,13 +11,13 @@ https://conda.anaconda.org/conda-forge/noarch/font-ttf-ubuntu-0.83-h77eed37_2.co https://conda.anaconda.org/conda-forge/linux-64/ld_impl_linux-64-2.40-hf3520f5_7.conda#b80f2f396ca2c28b8c14c437a4ed1e74 https://conda.anaconda.org/conda-forge/noarch/tzdata-2024a-h0c530f3_0.conda#161081fc7cec0bfda0d86d7cb595f8d8 https://conda.anaconda.org/conda-forge/noarch/fonts-conda-forge-1-0.tar.bz2#f766549260d6815b0c52253f1fb1bb29 -https://conda.anaconda.org/conda-forge/linux-64/libgomp-13.2.0-h77fa898_13.conda#d370d1855cca14dff6a819c90c77497c +https://conda.anaconda.org/conda-forge/linux-64/libgomp-14.1.0-h77fa898_0.conda#ae061a5ed5f05818acdf9adab72c146d https://conda.anaconda.org/conda-forge/linux-64/_openmp_mutex-4.5-2_gnu.tar.bz2#73aaf86a425cc6e73fcf236a5a46396d https://conda.anaconda.org/conda-forge/noarch/fonts-conda-ecosystem-1-0.tar.bz2#fee5683a3f04bd15cbd8318b096a27ab -https://conda.anaconda.org/conda-forge/linux-64/libgcc-ng-13.2.0-h77fa898_13.conda#9358cdd61ef0d600d2a0dde2d53b006c -https://conda.anaconda.org/conda-forge/linux-64/alsa-lib-1.2.11-hd590300_1.conda#0bb492cca54017ea314b809b1ee3a176 -https://conda.anaconda.org/conda-forge/linux-64/bzip2-1.0.8-hd590300_5.conda#69b8b6202a07720f448be700e300ccf4 -https://conda.anaconda.org/conda-forge/linux-64/c-ares-1.28.1-hd590300_0.conda#dcde58ff9a1f30b0037a2315d1846d1f +https://conda.anaconda.org/conda-forge/linux-64/libgcc-ng-14.1.0-h77fa898_0.conda#ca0fad6a41ddaef54a153b78eccb5037 +https://conda.anaconda.org/conda-forge/linux-64/alsa-lib-1.2.12-h4ab18f5_0.conda#7ed427f0871fd41cb1d9c17727c17589 +https://conda.anaconda.org/conda-forge/linux-64/bzip2-1.0.8-h4bc722e_7.conda#62ee74e96c5ebb0af99386de58cf9553 +https://conda.anaconda.org/conda-forge/linux-64/c-ares-1.32.3-h4bc722e_0.conda#7624e34ee6baebfc80d67bac76cc9d9d https://conda.anaconda.org/conda-forge/linux-64/giflib-5.2.2-hd590300_0.conda#3bf7b9fd5a7136126e0234db4b87c8b6 https://conda.anaconda.org/conda-forge/linux-64/keyutils-1.6.1-h166bdaf_0.tar.bz2#30186d27e2c9fa62b45fb1476b7200e3 https://conda.anaconda.org/conda-forge/linux-64/libdeflate-1.20-hd590300_0.conda#8e88f9389f1165d7c0936fe40d9a9a79 @@ -27,13 +27,13 @@ https://conda.anaconda.org/conda-forge/linux-64/libffi-3.4.2-h7f98852_5.tar.bz2# https://conda.anaconda.org/conda-forge/linux-64/libiconv-1.17-hd590300_2.conda#d66573916ffcf376178462f1b61c941e https://conda.anaconda.org/conda-forge/linux-64/libjpeg-turbo-3.0.0-hd590300_1.conda#ea25936bb4080d843790b586850f82b8 https://conda.anaconda.org/conda-forge/linux-64/libnsl-2.0.1-hd590300_0.conda#30fd6e37fe21f86f4bd26d6ee73eeec7 -https://conda.anaconda.org/conda-forge/linux-64/libstdcxx-ng-13.2.0-hc0a3c3a_13.conda#1053882642ed5bbc799e1e866ff86826 +https://conda.anaconda.org/conda-forge/linux-64/libstdcxx-ng-14.1.0-hc0a3c3a_0.conda#1cb187a157136398ddbaae90713e2498 https://conda.anaconda.org/conda-forge/linux-64/libuuid-2.38.1-h0b41bf4_0.conda#40b61aab5c7ba9ff276c41cfffe6b80b https://conda.anaconda.org/conda-forge/linux-64/libwebp-base-1.4.0-hd590300_0.conda#b26e8aa824079e1be0294e7152ca4559 https://conda.anaconda.org/conda-forge/linux-64/libxcrypt-4.4.36-hd590300_1.conda#5aa797f8787fe7a17d1b0821485b5adc -https://conda.anaconda.org/conda-forge/linux-64/libzlib-1.2.13-h4ab18f5_6.conda#27329162c0dc732bcf67a4e0cd488125 +https://conda.anaconda.org/conda-forge/linux-64/libzlib-1.3.1-h4ab18f5_1.conda#57d7dc60e9325e3de37ff8dffd18e814 https://conda.anaconda.org/conda-forge/linux-64/ncurses-6.5-h59595ed_0.conda#fcea371545eda051b6deafb24889fc69 -https://conda.anaconda.org/conda-forge/linux-64/openssl-3.3.1-h4ab18f5_1.conda#b1e9d076f14e8d776213fd5047b4c3d9 +https://conda.anaconda.org/conda-forge/linux-64/openssl-3.3.1-h4bc722e_2.conda#e1b454497f9f7c1147fdde4b53f1b512 https://conda.anaconda.org/conda-forge/linux-64/pthread-stubs-0.4-h36c2ea0_1001.tar.bz2#22dad4df6e8630e8dff2428f6f6a7036 https://conda.anaconda.org/conda-forge/linux-64/xorg-inputproto-2.3.2-h7f98852_1002.tar.bz2#bcd1b3396ec6960cbc1d2855a9e60b2b https://conda.anaconda.org/conda-forge/linux-64/xorg-kbproto-1.0.7-h7f98852_1002.tar.bz2#4b230e8381279d76131116660f5a241a @@ -47,48 +47,48 @@ https://conda.anaconda.org/conda-forge/linux-64/xorg-xproto-7.0.31-h7f98852_1007 https://conda.anaconda.org/conda-forge/linux-64/xz-5.2.6-h166bdaf_0.tar.bz2#2161070d867d1b1204ea749c8eec4ef0 https://conda.anaconda.org/conda-forge/linux-64/expat-2.6.2-h59595ed_0.conda#53fb86322bdb89496d7579fe3f02fd61 https://conda.anaconda.org/conda-forge/linux-64/graphite2-1.3.13-h59595ed_1003.conda#f87c7b7c2cb45f323ffbce941c78ab7c -https://conda.anaconda.org/conda-forge/linux-64/icu-73.2-h59595ed_0.conda#cc47e1facc155f91abd89b11e48e72ff +https://conda.anaconda.org/conda-forge/linux-64/icu-75.1-he02047a_0.conda#8b189310083baabfb622af68fd9d3ae3 https://conda.anaconda.org/conda-forge/linux-64/lerc-4.0.0-h27087fc_0.tar.bz2#76bbff344f0134279f225174e9064c8f https://conda.anaconda.org/conda-forge/linux-64/libedit-3.1.20191231-he28a2e2_2.tar.bz2#4d331e44109e3f0e19b4cb8f9b82f3e1 https://conda.anaconda.org/conda-forge/linux-64/libnghttp2-1.58.0-h47da74e_1.conda#700ac6ea6d53d5510591c4344d5c989a https://conda.anaconda.org/conda-forge/linux-64/libpng-1.6.43-h2797004_0.conda#009981dd9cfcaa4dbfa25ffaed86bcae https://conda.anaconda.org/conda-forge/linux-64/libsqlite-3.46.0-hde9e2c9_0.conda#18aa975d2094c34aef978060ae7da7d8 https://conda.anaconda.org/conda-forge/linux-64/libssh2-1.11.0-h0841786_0.conda#1f5a58e686b13bcfde88b93f547d23fe -https://conda.anaconda.org/conda-forge/linux-64/libxcb-1.15-h0b41bf4_0.conda#33277193f5b92bad9fdd230eb700929c -https://conda.anaconda.org/conda-forge/linux-64/pcre2-10.43-hcad00b1_0.conda#8292dea9e022d9610a11fce5e0896ed8 +https://conda.anaconda.org/conda-forge/linux-64/libxcb-1.16-hd590300_0.conda#151cba22b85a989c2d6ef9633ffee1e4 +https://conda.anaconda.org/conda-forge/linux-64/pcre2-10.44-h0f59acf_0.conda#3914f7ac1761dce57102c72ca7c35d01 https://conda.anaconda.org/conda-forge/linux-64/perl-5.32.1-7_hd590300_perl5.conda#f2cfec9406850991f4e3d960cc9e3321 https://conda.anaconda.org/conda-forge/linux-64/pixman-0.43.2-h59595ed_0.conda#71004cbf7924e19c02746ccde9fd7123 https://conda.anaconda.org/conda-forge/linux-64/readline-8.2-h8228510_1.conda#47d31b792659ce70f470b5c82fdfb7a4 https://conda.anaconda.org/conda-forge/linux-64/tk-8.6.13-noxft_h4845f30_101.conda#d453b98d9c83e71da0741bb0ff4d76bc https://conda.anaconda.org/conda-forge/linux-64/xorg-fixesproto-5.0-h7f98852_1002.tar.bz2#65ad6e1eb4aed2b0611855aff05e04f6 https://conda.anaconda.org/conda-forge/linux-64/xorg-libsm-1.2.4-h7391055_0.conda#93ee23f12bc2e684548181256edd2cf6 -https://conda.anaconda.org/conda-forge/linux-64/zlib-1.2.13-h4ab18f5_6.conda#559d338a4234c2ad6e676f460a093e67 +https://conda.anaconda.org/conda-forge/linux-64/zlib-1.3.1-h4ab18f5_1.conda#9653f1bf3766164d0e65fa723cabbc54 https://conda.anaconda.org/conda-forge/linux-64/zstd-1.5.6-ha6fb4c9_0.conda#4d056880988120e29d75bfff282e0f45 -https://conda.anaconda.org/bioconda/linux-64/bwa-0.7.18-he4a0461_0.tar.bz2#848d5a392a3a38545c42b1a079ca27c0 +https://conda.anaconda.org/bioconda/linux-64/bwa-0.7.18-he4a0461_1.tar.bz2#4ecde7d4a03fabe440a90aea1389d62d https://conda.anaconda.org/conda-forge/linux-64/freetype-2.12.1-h267a509_2.conda#9ae35c3d96db2c94ce0cef86efdfa2cb https://conda.anaconda.org/conda-forge/linux-64/krb5-1.21.3-h659f571_0.conda#3f43953b7d3fb3aaa1d0d0723d91e368 -https://conda.anaconda.org/conda-forge/linux-64/libglib-2.80.2-hf974151_0.conda#72724f6a78ecb15559396966226d5838 +https://conda.anaconda.org/conda-forge/linux-64/libglib-2.80.3-h8a4344b_1.conda#6ea440297aacee4893f02ad759e6ffbc https://conda.anaconda.org/conda-forge/linux-64/libtiff-4.6.0-h1dd3fc0_3.conda#66f03896ffbe1a110ffda05c7a856504 -https://conda.anaconda.org/conda-forge/linux-64/python-3.12.3-hab00c5b_0_cpython.conda#2540b74d304f71d3e89c81209db4db84 -https://conda.anaconda.org/conda-forge/linux-64/xorg-libx11-1.8.9-h8ee46fc_0.conda#077b6e8ad6a3ddb741fce2496dd01bec +https://conda.anaconda.org/conda-forge/linux-64/python-3.12.4-h194c7f8_0_cpython.conda#d73490214f536cccb5819e9873048c92 +https://conda.anaconda.org/conda-forge/linux-64/xorg-libx11-1.8.9-hb711507_1.conda#4a6d410296d7e39f00bacdee7df046e9 https://conda.anaconda.org/conda-forge/linux-64/fontconfig-2.14.2-h14ed4e7_0.conda#0f69b688f52ff6da70bccb7ff7001d1d https://conda.anaconda.org/conda-forge/linux-64/lcms2-2.16-hb7c19ff_0.conda#51bb7010fc86f70eee639b4bb7a894f5 https://conda.anaconda.org/conda-forge/linux-64/libcups-2.3.3-h4637d8d_4.conda#d4529f4dff3057982a7617c7ac58fde3 -https://conda.anaconda.org/conda-forge/linux-64/libcurl-8.8.0-hca28451_0.conda#f21c27f076a07907e70c49bb57bd0f20 -https://conda.anaconda.org/conda-forge/noarch/setuptools-70.1.1-pyhd8ed1ab_0.conda#985e9e86e1b0fc75a74a9bfab9309ef7 +https://conda.anaconda.org/conda-forge/linux-64/libcurl-8.9.0-hdb1bdb2_0.conda#5badfbdb2688d8aaca7bd3c98d557b97 +https://conda.anaconda.org/conda-forge/noarch/setuptools-71.0.4-pyhd8ed1ab_0.conda#ee78ac9c720d0d02fcfd420866b82ab1 https://conda.anaconda.org/bioconda/noarch/snakemake-wrapper-utils-0.6.2-pyhdfd78af_0.tar.bz2#fd8759bbd04116eace828c4fab906096 https://conda.anaconda.org/conda-forge/noarch/wheel-0.43.0-pyhd8ed1ab_1.conda#0b5293a157c2b5cd513dd1b03d8d3aae https://conda.anaconda.org/conda-forge/linux-64/xorg-libxext-1.3.4-h0b41bf4_2.conda#82b6df12252e6f32402b96dacc656fec https://conda.anaconda.org/conda-forge/linux-64/xorg-libxfixes-5.0.3-h7f98852_1004.tar.bz2#e9a21aa4d5e3e5f1aed71e8cefd46b6a https://conda.anaconda.org/conda-forge/linux-64/xorg-libxrender-0.9.11-hd590300_0.conda#ed67c36f215b310412b2af935bf3e530 https://conda.anaconda.org/conda-forge/linux-64/xorg-libxt-1.3.0-hd590300_1.conda#ae92aab42726eb29d16488924f7312cb -https://conda.anaconda.org/conda-forge/linux-64/cairo-1.18.0-h3faef2a_0.conda#f907bb958910dc404647326ca80c263e -https://conda.anaconda.org/bioconda/linux-64/htslib-1.20-h5efdd21_1.tar.bz2#451deefa67e250cf3268a484d9734465 +https://conda.anaconda.org/conda-forge/linux-64/cairo-1.18.0-hebfffa5_3.conda#fceaedf1cdbcb02df9699a0d9b005292 +https://conda.anaconda.org/bioconda/linux-64/htslib-1.20-h5efdd21_2.tar.bz2#f0923cdb85b44dc77bdead8018645ea9 https://conda.anaconda.org/conda-forge/noarch/pip-24.0-pyhd8ed1ab_0.conda#f586ac1e56c8638b64f9c8122a7b8a67 https://conda.anaconda.org/conda-forge/linux-64/xorg-libxi-1.7.10-h7f98852_0.tar.bz2#e77615e5141cad5a2acaa043d1cf0ca5 -https://conda.anaconda.org/conda-forge/linux-64/harfbuzz-8.5.0-hfac3d4d_0.conda#f5126317dd0ce0ba26945e411ecc6960 -https://conda.anaconda.org/bioconda/linux-64/samtools-1.20-h50ea8bc_0.tar.bz2#7b3b1d0feea64e7e211ae24e7cd126d8 -https://conda.anaconda.org/conda-forge/linux-64/xorg-libxtst-1.2.3-h7f98852_1002.tar.bz2#a220b1a513e19d5cb56c1311d44f12e6 -https://conda.anaconda.org/conda-forge/linux-64/openjdk-22.0.1-hb622114_0.conda#cddebf320a874489f4e231b45e66c1e1 -https://conda.anaconda.org/bioconda/noarch/fgbio-minimal-2.2.1-hdfd78af_0.tar.bz2#baed6bfb163c27c118bbbea2ece183bb +https://conda.anaconda.org/conda-forge/linux-64/harfbuzz-9.0.0-hda332d3_1.conda#76b32dcf243444aea9c6b804bcfa40b8 +https://conda.anaconda.org/bioconda/linux-64/samtools-1.20-h50ea8bc_1.tar.bz2#1a4c52f8079fea1b18b3e4bd329bab3a +https://conda.anaconda.org/conda-forge/linux-64/xorg-libxtst-1.2.4-h4bc722e_0.conda#4561491e71d04bfe58d4f0ce5329656e +https://conda.anaconda.org/conda-forge/linux-64/openjdk-22.0.1-h8651b0f_1.conda#672153e7c3d4f70bc65993f3ee513768 +https://conda.anaconda.org/bioconda/noarch/fgbio-minimal-2.3.0-hdfd78af_0.tar.bz2#48e39a611203a971c32302c8d0151432 https://conda.anaconda.org/bioconda/noarch/picard-slim-3.2.0-hdfd78af_0.tar.bz2#b96f183b2167c69b4784ef921bef19ab diff --git a/bio/bwa/mem/environment.yaml b/bio/bwa/mem/environment.yaml index 7b9aac443f8..8f3142413eb 100644 --- a/bio/bwa/mem/environment.yaml +++ b/bio/bwa/mem/environment.yaml @@ -4,7 +4,7 @@ channels: - nodefaults dependencies: - bwa =0.7.18 - - fgbio-minimal =2.2.1 + - fgbio-minimal =2.3.0 - samtools =1.20 - picard-slim =3.2.0 - snakemake-wrapper-utils =0.6.2 From bc0b80db175c25a04cc2c4a3cd665f6be297741b Mon Sep 17 00:00:00 2001 From: "snakedeploy-bot[bot]" <115615832+snakedeploy-bot[bot]@users.noreply.github.com> Date: Fri, 26 Jul 2024 01:55:32 +0000 Subject: [PATCH 07/62] perf: autobump bio/blast/blastn (#3080) Automatic bump of bio/blast/blastn. --------- Co-authored-by: snakedeploy-bot[bot] <115615832+snakedeploy-bot[bot]@users.noreply.github.com> --- bio/blast/blastn/environment.linux-64.pin.txt | 89 +++++++------------ bio/blast/blastn/environment.yaml | 2 +- 2 files changed, 33 insertions(+), 58 deletions(-) diff --git a/bio/blast/blastn/environment.linux-64.pin.txt b/bio/blast/blastn/environment.linux-64.pin.txt index aaf65944f9d..d541457b488 100644 --- a/bio/blast/blastn/environment.linux-64.pin.txt +++ b/bio/blast/blastn/environment.linux-64.pin.txt @@ -3,84 +3,59 @@ # platform: linux-64 @EXPLICIT https://conda.anaconda.org/conda-forge/linux-64/_libgcc_mutex-0.1-conda_forge.tar.bz2#d7c89558ba9fa0495403155b64376d81 -https://conda.anaconda.org/conda-forge/linux-64/ca-certificates-2023.7.22-hbcca054_0.conda#a73ecd2988327ad4c8f2c331482917f2 -https://conda.anaconda.org/conda-forge/linux-64/libstdcxx-ng-13.2.0-h7e041cc_3.conda#937eaed008f6bf2191c5fe76f87755e9 -https://conda.anaconda.org/conda-forge/linux-64/libgomp-13.2.0-h807b86a_3.conda#7124cbb46b13d395bdde68f2d215c989 +https://conda.anaconda.org/conda-forge/linux-64/ca-certificates-2024.7.4-hbcca054_0.conda#23ab7665c5f63cfb9f1f6195256daac6 +https://conda.anaconda.org/conda-forge/linux-64/libgomp-14.1.0-h77fa898_0.conda#ae061a5ed5f05818acdf9adab72c146d https://conda.anaconda.org/conda-forge/linux-64/_openmp_mutex-4.5-2_gnu.tar.bz2#73aaf86a425cc6e73fcf236a5a46396d -https://conda.anaconda.org/conda-forge/linux-64/libgcc-ng-13.2.0-h807b86a_3.conda#23fdf1fef05baeb7eadc2aed5fb0011f -https://conda.anaconda.org/conda-forge/linux-64/bzip2-1.0.8-hd590300_5.conda#69b8b6202a07720f448be700e300ccf4 -https://conda.anaconda.org/conda-forge/linux-64/c-ares-1.21.0-hd590300_0.conda#c06fa0440048270817b9e3142cc661bf -https://conda.anaconda.org/conda-forge/linux-64/gettext-0.21.1-h27087fc_0.tar.bz2#14947d8770185e5153fdd04d4673ed37 -https://conda.anaconda.org/conda-forge/linux-64/icu-70.1-h27087fc_0.tar.bz2#87473a15119779e021c314249d4b4aed +https://conda.anaconda.org/conda-forge/linux-64/libgcc-ng-14.1.0-h77fa898_0.conda#ca0fad6a41ddaef54a153b78eccb5037 +https://conda.anaconda.org/conda-forge/linux-64/bzip2-1.0.8-h4bc722e_7.conda#62ee74e96c5ebb0af99386de58cf9553 +https://conda.anaconda.org/conda-forge/linux-64/c-ares-1.32.3-h4bc722e_0.conda#7624e34ee6baebfc80d67bac76cc9d9d +https://conda.anaconda.org/conda-forge/linux-64/gettext-tools-0.22.5-h59595ed_2.conda#985f2f453fb72408d6b6f1be0f324033 https://conda.anaconda.org/conda-forge/linux-64/keyutils-1.6.1-h166bdaf_0.tar.bz2#30186d27e2c9fa62b45fb1476b7200e3 -https://conda.anaconda.org/conda-forge/linux-64/libev-4.33-h516909a_1.tar.bz2#6f8720dff19e17ce5d48cfe7f3d2f0a3 -https://conda.anaconda.org/conda-forge/linux-64/libiconv-1.17-h166bdaf_0.tar.bz2#b62b52da46c39ee2bc3c162ac7f1804d -https://conda.anaconda.org/conda-forge/linux-64/libnsl-2.0.1-hd590300_0.conda#30fd6e37fe21f86f4bd26d6ee73eeec7 +https://conda.anaconda.org/conda-forge/linux-64/libev-4.33-hd590300_2.conda#172bf1cd1ff8629f2b1179945ed45055 +https://conda.anaconda.org/conda-forge/linux-64/libgettextpo-0.22.5-h59595ed_2.conda#172bcc51059416e7ce99e7b528cede83 +https://conda.anaconda.org/conda-forge/linux-64/libstdcxx-ng-14.1.0-hc0a3c3a_0.conda#1cb187a157136398ddbaae90713e2498 https://conda.anaconda.org/conda-forge/linux-64/libunistring-0.9.10-h7f98852_0.tar.bz2#7245a044b4a1980ed83196176b78b73a -https://conda.anaconda.org/conda-forge/linux-64/libzlib-1.2.13-hd590300_5.conda#f36c115f1ee199da648e0597ec2047ad -https://conda.anaconda.org/conda-forge/linux-64/ncurses-6.4-h59595ed_2.conda#7dbaa197d7ba6032caf7ae7f32c1efa0 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+https://conda.anaconda.org/bioconda/linux-64/entrez-direct-22.4-he881be0_0.tar.bz2#0994f567f11543b7aea1afce884c2ce6 +https://conda.anaconda.org/bioconda/linux-64/blast-2.16.0-h6f7f691_0.tar.bz2#098092890e9c94de10a3fe827339bc16 diff --git a/bio/blast/blastn/environment.yaml b/bio/blast/blastn/environment.yaml index d6a2cb7075f..97060d39ce6 100644 --- a/bio/blast/blastn/environment.yaml +++ b/bio/blast/blastn/environment.yaml @@ -3,4 +3,4 @@ channels: - bioconda - nodefaults dependencies: - - blast =2.15.0 + - blast =2.16.0 From f178d5f1da9a8f420a1e1f8f08053f3983dc11e0 Mon Sep 17 00:00:00 2001 From: "snakedeploy-bot[bot]" <115615832+snakedeploy-bot[bot]@users.noreply.github.com> Date: Fri, 26 Jul 2024 02:58:03 +0000 Subject: [PATCH 08/62] perf: autobump bio/entrez/efetch (#3081) Automatic bump of bio/entrez/efetch. --------- Co-authored-by: snakedeploy-bot[bot] <115615832+snakedeploy-bot[bot]@users.noreply.github.com> --- bio/entrez/efetch/environment.linux-64.pin.txt | 16 ++++++++-------- bio/entrez/efetch/environment.yaml | 2 +- 2 files changed, 9 insertions(+), 9 deletions(-) diff --git a/bio/entrez/efetch/environment.linux-64.pin.txt b/bio/entrez/efetch/environment.linux-64.pin.txt index efa188c7b1e..1d37af61414 100644 --- a/bio/entrez/efetch/environment.linux-64.pin.txt +++ b/bio/entrez/efetch/environment.linux-64.pin.txt @@ -3,21 +3,21 @@ # platform: linux-64 @EXPLICIT https://conda.anaconda.org/conda-forge/linux-64/_libgcc_mutex-0.1-conda_forge.tar.bz2#d7c89558ba9fa0495403155b64376d81 -https://conda.anaconda.org/conda-forge/linux-64/ca-certificates-2024.6.2-hbcca054_0.conda#847c3c2905cc467cea52c24f9cfa8080 -https://conda.anaconda.org/conda-forge/linux-64/libstdcxx-ng-13.2.0-hc0a3c3a_7.conda#53ebd4c833fa01cb2c6353e99f905406 -https://conda.anaconda.org/conda-forge/linux-64/libgomp-13.2.0-h77fa898_7.conda#abf3fec87c2563697defa759dec3d639 +https://conda.anaconda.org/conda-forge/linux-64/ca-certificates-2024.7.4-hbcca054_0.conda#23ab7665c5f63cfb9f1f6195256daac6 +https://conda.anaconda.org/conda-forge/linux-64/libgomp-14.1.0-h77fa898_0.conda#ae061a5ed5f05818acdf9adab72c146d https://conda.anaconda.org/conda-forge/linux-64/_openmp_mutex-4.5-2_gnu.tar.bz2#73aaf86a425cc6e73fcf236a5a46396d -https://conda.anaconda.org/conda-forge/linux-64/libgcc-ng-13.2.0-h77fa898_7.conda#72ec1b1b04c4d15d4204ece1ecea5978 +https://conda.anaconda.org/conda-forge/linux-64/libgcc-ng-14.1.0-h77fa898_0.conda#ca0fad6a41ddaef54a153b78eccb5037 https://conda.anaconda.org/conda-forge/linux-64/gettext-tools-0.22.5-h59595ed_2.conda#985f2f453fb72408d6b6f1be0f324033 -https://conda.anaconda.org/conda-forge/linux-64/libasprintf-0.22.5-h661eb56_2.conda#dd197c968bf9760bba0031888d431ede https://conda.anaconda.org/conda-forge/linux-64/libgettextpo-0.22.5-h59595ed_2.conda#172bcc51059416e7ce99e7b528cede83 +https://conda.anaconda.org/conda-forge/linux-64/libstdcxx-ng-14.1.0-hc0a3c3a_0.conda#1cb187a157136398ddbaae90713e2498 https://conda.anaconda.org/conda-forge/linux-64/libunistring-0.9.10-h7f98852_0.tar.bz2#7245a044b4a1980ed83196176b78b73a https://conda.anaconda.org/conda-forge/linux-64/libzlib-1.3.1-h4ab18f5_1.conda#57d7dc60e9325e3de37ff8dffd18e814 -https://conda.anaconda.org/conda-forge/linux-64/openssl-3.3.1-h4ab18f5_0.conda#a41fa0e391cc9e0d6b78ac69ca047a6c -https://conda.anaconda.org/conda-forge/linux-64/libasprintf-devel-0.22.5-h661eb56_2.conda#02e41ab5834dcdcc8590cf29d9526f50 +https://conda.anaconda.org/conda-forge/linux-64/openssl-3.3.1-h4bc722e_2.conda#e1b454497f9f7c1147fdde4b53f1b512 +https://conda.anaconda.org/conda-forge/linux-64/libasprintf-0.22.5-h661eb56_2.conda#dd197c968bf9760bba0031888d431ede https://conda.anaconda.org/conda-forge/linux-64/libgettextpo-devel-0.22.5-h59595ed_2.conda#b63d9b6da3653179a278077f0de20014 https://conda.anaconda.org/conda-forge/linux-64/zlib-1.3.1-h4ab18f5_1.conda#9653f1bf3766164d0e65fa723cabbc54 +https://conda.anaconda.org/conda-forge/linux-64/libasprintf-devel-0.22.5-h661eb56_2.conda#02e41ab5834dcdcc8590cf29d9526f50 https://conda.anaconda.org/conda-forge/linux-64/gettext-0.22.5-h59595ed_2.conda#219ba82e95d7614cf7140d2a4afc0926 https://conda.anaconda.org/conda-forge/linux-64/libidn2-2.3.7-hd590300_0.conda#2b7b0d827c6447cc1d85dc06d5b5de46 https://conda.anaconda.org/conda-forge/linux-64/wget-1.21.4-hda4d442_0.conda#361e96b664eac64a33c20dfd11affbff -https://conda.anaconda.org/bioconda/linux-64/entrez-direct-22.1-he881be0_0.tar.bz2#57b4957374cfeb937f02aa75670b02fa +https://conda.anaconda.org/bioconda/linux-64/entrez-direct-22.4-he881be0_0.tar.bz2#0994f567f11543b7aea1afce884c2ce6 diff --git a/bio/entrez/efetch/environment.yaml b/bio/entrez/efetch/environment.yaml index ced613660d9..3c6a560fb5b 100644 --- a/bio/entrez/efetch/environment.yaml +++ b/bio/entrez/efetch/environment.yaml @@ -3,4 +3,4 @@ channels: - bioconda - nodefaults dependencies: - - entrez-direct =22.1 + - entrez-direct =22.4 From b902adfb65d0ea18dc557b25aa98031a394a99c8 Mon Sep 17 00:00:00 2001 From: "snakedeploy-bot[bot]" <115615832+snakedeploy-bot[bot]@users.noreply.github.com> Date: Fri, 26 Jul 2024 03:01:01 +0000 Subject: [PATCH 09/62] perf: autobump bio/fgbio/annotatebamwithumis (#3082) Automatic bump of bio/fgbio/annotatebamwithumis. --------- Co-authored-by: snakedeploy-bot[bot] <115615832+snakedeploy-bot[bot]@users.noreply.github.com> --- .../environment.linux-64.pin.txt | 184 +++++++++--------- .../annotatebamwithumis/environment.yaml | 2 +- 2 files changed, 94 insertions(+), 92 deletions(-) diff --git a/bio/fgbio/annotatebamwithumis/environment.linux-64.pin.txt b/bio/fgbio/annotatebamwithumis/environment.linux-64.pin.txt index ac84902a82f..e440f474fac 100644 --- a/bio/fgbio/annotatebamwithumis/environment.linux-64.pin.txt +++ b/bio/fgbio/annotatebamwithumis/environment.linux-64.pin.txt @@ -4,51 +4,46 @@ @EXPLICIT https://conda.anaconda.org/conda-forge/linux-64/_libgcc_mutex-0.1-conda_forge.tar.bz2#d7c89558ba9fa0495403155b64376d81 https://conda.anaconda.org/conda-forge/noarch/_r-mutex-1.0.1-anacondar_1.tar.bz2#19f9db5f4f1b7f5ef5f6d67207f25f38 -https://conda.anaconda.org/conda-forge/linux-64/ca-certificates-2023.11.17-hbcca054_0.conda#01ffc8d36f9eba0ce0b3c1955fa780ee +https://conda.anaconda.org/conda-forge/noarch/_sysroot_linux-64_curr_repodata_hack-3-h69a702a_16.conda#1c005af0c6ff22814b7c52ee448d4bea +https://conda.anaconda.org/conda-forge/linux-64/ca-certificates-2024.7.4-hbcca054_0.conda#23ab7665c5f63cfb9f1f6195256daac6 https://conda.anaconda.org/conda-forge/noarch/font-ttf-dejavu-sans-mono-2.37-hab24e00_0.tar.bz2#0c96522c6bdaed4b1566d11387caaf45 https://conda.anaconda.org/conda-forge/noarch/font-ttf-inconsolata-3.000-h77eed37_0.tar.bz2#34893075a5c9e55cdafac56607368fc6 https://conda.anaconda.org/conda-forge/noarch/font-ttf-source-code-pro-2.038-h77eed37_0.tar.bz2#4d59c254e01d9cde7957100457e2d5fb -https://conda.anaconda.org/conda-forge/noarch/font-ttf-ubuntu-0.83-h77eed37_1.conda#6185f640c43843e5ad6fd1c5372c3f80 -https://conda.anaconda.org/conda-forge/noarch/kernel-headers_linux-64-2.6.32-he073ed8_16.conda#7ca122655873935e02c91279c5b03c8c -https://conda.anaconda.org/conda-forge/linux-64/ld_impl_linux-64-2.40-h41732ed_0.conda#7aca3059a1729aa76c597603f10b0dd3 -https://conda.anaconda.org/conda-forge/noarch/libgcc-devel_linux-64-13.2.0-ha9c7c90_103.conda#db8cd1a871a07404d94f7dcc78c21a61 -https://conda.anaconda.org/conda-forge/noarch/libstdcxx-devel_linux-64-13.2.0-ha9c7c90_103.conda#46947f93254fdedc5ae0725b11ca3610 -https://conda.anaconda.org/conda-forge/linux-64/libstdcxx-ng-13.2.0-h7e041cc_3.conda#937eaed008f6bf2191c5fe76f87755e9 -https://conda.anaconda.org/conda-forge/noarch/tzdata-2023d-h0c530f3_0.conda#8dee24b8be2d9ff81e7bd4d7d97ff1b0 +https://conda.anaconda.org/conda-forge/noarch/font-ttf-ubuntu-0.83-h77eed37_2.conda#cbbe59391138ea5ad3658c76912e147f +https://conda.anaconda.org/conda-forge/linux-64/ld_impl_linux-64-2.40-hf3520f5_7.conda#b80f2f396ca2c28b8c14c437a4ed1e74 +https://conda.anaconda.org/conda-forge/noarch/libgcc-devel_linux-64-14.1.0-h5d3d1c9_100.conda#6d4f65dc440f7b3422113b135be19703 +https://conda.anaconda.org/conda-forge/noarch/libstdcxx-devel_linux-64-14.1.0-h5d3d1c9_100.conda#cedc62fd8c4cf28f23d3cd5db7839e99 +https://conda.anaconda.org/conda-forge/noarch/tzdata-2024a-h0c530f3_0.conda#161081fc7cec0bfda0d86d7cb595f8d8 https://conda.anaconda.org/conda-forge/noarch/fonts-conda-forge-1-0.tar.bz2#f766549260d6815b0c52253f1fb1bb29 -https://conda.anaconda.org/conda-forge/linux-64/libgomp-13.2.0-h807b86a_3.conda#7124cbb46b13d395bdde68f2d215c989 -https://conda.anaconda.org/conda-forge/noarch/sysroot_linux-64-2.12-he073ed8_16.conda#071ea8dceff4d30ac511f4a2f8437cd1 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Date: Fri, 26 Jul 2024 03:03:32 +0000 Subject: [PATCH 10/62] perf: autobump bio/fgbio/groupreadsbyumi (#3083) Automatic bump of bio/fgbio/groupreadsbyumi. --------- Co-authored-by: snakedeploy-bot[bot] <115615832+snakedeploy-bot[bot]@users.noreply.github.com> --- .../environment.linux-64.pin.txt | 184 +++++++++--------- bio/fgbio/groupreadsbyumi/environment.yaml | 2 +- 2 files changed, 94 insertions(+), 92 deletions(-) diff --git a/bio/fgbio/groupreadsbyumi/environment.linux-64.pin.txt b/bio/fgbio/groupreadsbyumi/environment.linux-64.pin.txt index 4595cc622df..226bb2965fd 100644 --- a/bio/fgbio/groupreadsbyumi/environment.linux-64.pin.txt +++ b/bio/fgbio/groupreadsbyumi/environment.linux-64.pin.txt @@ -4,51 +4,46 @@ @EXPLICIT https://conda.anaconda.org/conda-forge/linux-64/_libgcc_mutex-0.1-conda_forge.tar.bz2#d7c89558ba9fa0495403155b64376d81 https://conda.anaconda.org/conda-forge/noarch/_r-mutex-1.0.1-anacondar_1.tar.bz2#19f9db5f4f1b7f5ef5f6d67207f25f38 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b/bio/fgbio/collectduplexseqmetrics/environment.yaml index 14104bbc2ad..58044deabfa 100644 --- a/bio/fgbio/collectduplexseqmetrics/environment.yaml +++ b/bio/fgbio/collectduplexseqmetrics/environment.yaml @@ -3,5 +3,5 @@ channels: - bioconda - nodefaults dependencies: - - fgbio =2.2.1 + - fgbio =2.3.0 - snakemake-wrapper-utils =0.6.2 From 5727f2d1369ee5afe5fe0f3e5a051f81e51b553a Mon Sep 17 00:00:00 2001 From: "snakedeploy-bot[bot]" <115615832+snakedeploy-bot[bot]@users.noreply.github.com> Date: Fri, 26 Jul 2024 03:06:02 +0000 Subject: [PATCH 12/62] perf: autobump bio/fgbio/callmolecularconsensusreads (#3085) Automatic bump of bio/fgbio/callmolecularconsensusreads. --------- Co-authored-by: snakedeploy-bot[bot] <115615832+snakedeploy-bot[bot]@users.noreply.github.com> --- .../environment.linux-64.pin.txt | 184 +++++++++--------- .../environment.yaml | 2 +- 2 files changed, 94 insertions(+), 92 deletions(-) diff --git a/bio/fgbio/callmolecularconsensusreads/environment.linux-64.pin.txt 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+https://conda.anaconda.org/conda-forge/linux-64/r-tibble-3.2.1-r44hdb488b9_3.conda#03203ac70558ba5bb836d1cb641f1b87 +https://conda.anaconda.org/conda-forge/noarch/r-ggplot2-3.5.1-r44hc72bb7e_1.conda#c6209f7de229696ebd0086e7c27a02ac +https://conda.anaconda.org/bioconda/noarch/fgbio-2.3.0-hdfd78af_0.tar.bz2#2b0378bb6f00f8fb837886a807603e27 diff --git a/bio/fgbio/filterconsensusreads/environment.yaml b/bio/fgbio/filterconsensusreads/environment.yaml index f1f997b6554..997b5b62cfb 100644 --- a/bio/fgbio/filterconsensusreads/environment.yaml +++ b/bio/fgbio/filterconsensusreads/environment.yaml @@ -3,4 +3,4 @@ channels: - bioconda - nodefaults dependencies: - - fgbio =2.2.1 + - fgbio =2.3.0 From b23c95d9d12182f4e6234486b7ce4274272fa8be Mon Sep 17 00:00:00 2001 From: "snakedeploy-bot[bot]" <115615832+snakedeploy-bot[bot]@users.noreply.github.com> Date: Fri, 26 Jul 2024 03:09:23 +0000 Subject: [PATCH 14/62] perf: autobump bio/freebayes (#3087) Automatic bump of bio/freebayes. --------- Co-authored-by: snakedeploy-bot[bot] <115615832+snakedeploy-bot[bot]@users.noreply.github.com> --- bio/freebayes/environment.linux-64.pin.txt | 50 +++++++++++----------- bio/freebayes/environment.yaml | 2 +- 2 files changed, 26 insertions(+), 26 deletions(-) diff --git a/bio/freebayes/environment.linux-64.pin.txt b/bio/freebayes/environment.linux-64.pin.txt index 8ab7ef6b851..ad4b567af14 100644 --- a/bio/freebayes/environment.linux-64.pin.txt +++ b/bio/freebayes/environment.linux-64.pin.txt @@ -3,58 +3,58 @@ # platform: linux-64 @EXPLICIT https://conda.anaconda.org/conda-forge/linux-64/_libgcc_mutex-0.1-conda_forge.tar.bz2#d7c89558ba9fa0495403155b64376d81 -https://conda.anaconda.org/conda-forge/linux-64/ca-certificates-2024.2.2-hbcca054_0.conda#2f4327a1cbe7f022401b236e915a5fef -https://conda.anaconda.org/conda-forge/linux-64/ld_impl_linux-64-2.40-hf3520f5_1.conda#33b7851c39c25da14f6a233a8ccbeeca -https://conda.anaconda.org/conda-forge/linux-64/libstdcxx-ng-13.2.0-hc0a3c3a_7.conda#53ebd4c833fa01cb2c6353e99f905406 +https://conda.anaconda.org/conda-forge/linux-64/ca-certificates-2024.7.4-hbcca054_0.conda#23ab7665c5f63cfb9f1f6195256daac6 +https://conda.anaconda.org/conda-forge/linux-64/ld_impl_linux-64-2.40-hf3520f5_7.conda#b80f2f396ca2c28b8c14c437a4ed1e74 https://conda.anaconda.org/conda-forge/noarch/tzdata-2024a-h0c530f3_0.conda#161081fc7cec0bfda0d86d7cb595f8d8 -https://conda.anaconda.org/conda-forge/linux-64/libgomp-13.2.0-h77fa898_7.conda#abf3fec87c2563697defa759dec3d639 +https://conda.anaconda.org/conda-forge/linux-64/libgomp-14.1.0-h77fa898_0.conda#ae061a5ed5f05818acdf9adab72c146d https://conda.anaconda.org/conda-forge/linux-64/_openmp_mutex-4.5-2_gnu.tar.bz2#73aaf86a425cc6e73fcf236a5a46396d -https://conda.anaconda.org/conda-forge/linux-64/libgcc-ng-13.2.0-h77fa898_7.conda#72ec1b1b04c4d15d4204ece1ecea5978 -https://conda.anaconda.org/conda-forge/linux-64/bzip2-1.0.8-hd590300_5.conda#69b8b6202a07720f448be700e300ccf4 -https://conda.anaconda.org/conda-forge/linux-64/c-ares-1.28.1-hd590300_0.conda#dcde58ff9a1f30b0037a2315d1846d1f -https://conda.anaconda.org/conda-forge/linux-64/eigen-3.4.0-h00ab1b0_0.conda#b1b879d6d093f55dd40d58b5eb2f0699 -https://conda.anaconda.org/conda-forge/linux-64/jsoncpp-1.9.5-h4bd325d_1.tar.bz2#ae7f50dd1e78c7e78b5d2cf7062e559d +https://conda.anaconda.org/conda-forge/linux-64/libgcc-ng-14.1.0-h77fa898_0.conda#ca0fad6a41ddaef54a153b78eccb5037 +https://conda.anaconda.org/conda-forge/linux-64/bzip2-1.0.8-h4bc722e_7.conda#62ee74e96c5ebb0af99386de58cf9553 +https://conda.anaconda.org/conda-forge/linux-64/c-ares-1.32.3-h4bc722e_0.conda#7624e34ee6baebfc80d67bac76cc9d9d https://conda.anaconda.org/conda-forge/linux-64/keyutils-1.6.1-h166bdaf_0.tar.bz2#30186d27e2c9fa62b45fb1476b7200e3 https://conda.anaconda.org/conda-forge/linux-64/libdeflate-1.20-hd590300_0.conda#8e88f9389f1165d7c0936fe40d9a9a79 https://conda.anaconda.org/conda-forge/linux-64/libev-4.33-hd590300_2.conda#172bf1cd1ff8629f2b1179945ed45055 https://conda.anaconda.org/conda-forge/linux-64/libexpat-2.6.2-h59595ed_0.conda#e7ba12deb7020dd080c6c70e7b6f6a3d https://conda.anaconda.org/conda-forge/linux-64/libffi-3.4.2-h7f98852_5.tar.bz2#d645c6d2ac96843a2bfaccd2d62b3ac3 -https://conda.anaconda.org/conda-forge/linux-64/libgfortran5-13.2.0-hca663fb_7.conda#c0bd771f09a326fdcd95a60b617795bf +https://conda.anaconda.org/conda-forge/linux-64/libgfortran5-14.1.0-hc5f4f2c_0.conda#6456c2620c990cd8dde2428a27ba0bc5 https://conda.anaconda.org/conda-forge/linux-64/libnsl-2.0.1-hd590300_0.conda#30fd6e37fe21f86f4bd26d6ee73eeec7 +https://conda.anaconda.org/conda-forge/linux-64/libstdcxx-ng-14.1.0-hc0a3c3a_0.conda#1cb187a157136398ddbaae90713e2498 https://conda.anaconda.org/conda-forge/linux-64/libuuid-2.38.1-h0b41bf4_0.conda#40b61aab5c7ba9ff276c41cfffe6b80b https://conda.anaconda.org/conda-forge/linux-64/libxcrypt-4.4.36-hd590300_1.conda#5aa797f8787fe7a17d1b0821485b5adc https://conda.anaconda.org/conda-forge/linux-64/libzlib-1.2.13-h4ab18f5_6.conda#27329162c0dc732bcf67a4e0cd488125 https://conda.anaconda.org/conda-forge/linux-64/ncurses-6.5-h59595ed_0.conda#fcea371545eda051b6deafb24889fc69 -https://conda.anaconda.org/conda-forge/linux-64/openssl-3.3.0-h4ab18f5_3.conda#12ea6d0d4ed54530eaed18e4835c1f7c +https://conda.anaconda.org/conda-forge/linux-64/openssl-3.3.1-h4bc722e_2.conda#e1b454497f9f7c1147fdde4b53f1b512 https://conda.anaconda.org/conda-forge/linux-64/sed-4.8-he412f7d_0.tar.bz2#7362f0042e95681f5d371c46c83ebd08 -https://conda.anaconda.org/bioconda/linux-64/wfa2-lib-2.3.5-h4ac6f70_0.tar.bz2#6e462242b628a90a06fe64c8e8fac0cf https://conda.anaconda.org/conda-forge/linux-64/xz-5.2.6-h166bdaf_0.tar.bz2#2161070d867d1b1204ea749c8eec4ef0 -https://conda.anaconda.org/bioconda/linux-64/bedtools-2.31.1-hf5e1c6e_1.tar.bz2#2066287e826a2ff469fa0b62b24b6059 +https://conda.anaconda.org/bioconda/linux-64/bedtools-2.31.1-hf5e1c6e_2.tar.bz2#55aacbd977c83d6d4849c91310ef48c5 +https://conda.anaconda.org/conda-forge/linux-64/eigen-3.4.0-h00ab1b0_0.conda#b1b879d6d093f55dd40d58b5eb2f0699 +https://conda.anaconda.org/conda-forge/linux-64/jsoncpp-1.9.5-h4bd325d_1.tar.bz2#ae7f50dd1e78c7e78b5d2cf7062e559d https://conda.anaconda.org/conda-forge/linux-64/libedit-3.1.20191231-he28a2e2_2.tar.bz2#4d331e44109e3f0e19b4cb8f9b82f3e1 -https://conda.anaconda.org/conda-forge/linux-64/libgfortran-ng-13.2.0-h69a702a_7.conda#1b84f26d9f4f6026e179e7805d5a15cd +https://conda.anaconda.org/conda-forge/linux-64/libgfortran-ng-14.1.0-h69a702a_0.conda#f4ca84fbd6d06b0a052fb2d5b96dde41 https://conda.anaconda.org/conda-forge/linux-64/libnghttp2-1.58.0-h47da74e_1.conda#700ac6ea6d53d5510591c4344d5c989a -https://conda.anaconda.org/conda-forge/linux-64/libsqlite-3.45.3-h2797004_0.conda#b3316cbe90249da4f8e84cd66e1cc55b +https://conda.anaconda.org/conda-forge/linux-64/libsqlite-3.46.0-hde9e2c9_0.conda#18aa975d2094c34aef978060ae7da7d8 https://conda.anaconda.org/conda-forge/linux-64/libssh2-1.11.0-h0841786_0.conda#1f5a58e686b13bcfde88b93f547d23fe https://conda.anaconda.org/conda-forge/linux-64/perl-5.32.1-7_hd590300_perl5.conda#f2cfec9406850991f4e3d960cc9e3321 https://conda.anaconda.org/conda-forge/linux-64/readline-8.2-h8228510_1.conda#47d31b792659ce70f470b5c82fdfb7a4 https://conda.anaconda.org/conda-forge/linux-64/tk-8.6.13-noxft_h4845f30_101.conda#d453b98d9c83e71da0741bb0ff4d76bc +https://conda.anaconda.org/bioconda/linux-64/wfa2-lib-2.3.5-h4ac6f70_0.tar.bz2#6e462242b628a90a06fe64c8e8fac0cf https://conda.anaconda.org/conda-forge/linux-64/zlib-1.2.13-h4ab18f5_6.conda#559d338a4234c2ad6e676f460a093e67 https://conda.anaconda.org/conda-forge/linux-64/zstd-1.5.6-ha6fb4c9_0.conda#4d056880988120e29d75bfff282e0f45 -https://conda.anaconda.org/conda-forge/linux-64/krb5-1.21.2-h659d440_0.conda#cd95826dbd331ed1be26bdf401432844 -https://conda.anaconda.org/conda-forge/linux-64/libopenblas-0.3.27-pthreads_h413a1c8_0.conda#a356024784da6dfd4683dc5ecf45b155 -https://conda.anaconda.org/conda-forge/linux-64/parallel-20240522-ha770c72_0.conda#95444bc23d494d0b06405bea54c7cd1f +https://conda.anaconda.org/conda-forge/linux-64/krb5-1.21.3-h659f571_0.conda#3f43953b7d3fb3aaa1d0d0723d91e368 +https://conda.anaconda.org/conda-forge/linux-64/libopenblas-0.3.27-pthreads_hac2b453_1.conda#ae05ece66d3924ac3d48b4aa3fa96cec +https://conda.anaconda.org/conda-forge/linux-64/parallel-20240722-ha770c72_0.conda#acad361a391f190dc2fa629a2814fdcf https://conda.anaconda.org/conda-forge/linux-64/python-3.12.3-hab00c5b_0_cpython.conda#2540b74d304f71d3e89c81209db4db84 -https://conda.anaconda.org/conda-forge/linux-64/libblas-3.9.0-22_linux64_openblas.conda#1a2a0cd3153464fee6646f3dd6dad9b8 -https://conda.anaconda.org/conda-forge/linux-64/libcurl-8.8.0-hca28451_0.conda#f21c27f076a07907e70c49bb57bd0f20 -https://conda.anaconda.org/conda-forge/noarch/setuptools-70.0.0-pyhd8ed1ab_0.conda#c8ddb4f34a208df4dd42509a0f6a1c89 +https://conda.anaconda.org/conda-forge/linux-64/libblas-3.9.0-23_linux64_openblas.conda#96c8450a40aa2b9733073a9460de972c +https://conda.anaconda.org/conda-forge/linux-64/libcurl-8.8.0-hca28451_1.conda#b8afb3e3cb3423cc445cf611ab95fdb0 +https://conda.anaconda.org/conda-forge/noarch/setuptools-71.0.4-pyhd8ed1ab_0.conda#ee78ac9c720d0d02fcfd420866b82ab1 https://conda.anaconda.org/bioconda/noarch/snakemake-wrapper-utils-0.6.2-pyhdfd78af_0.tar.bz2#fd8759bbd04116eace828c4fab906096 https://conda.anaconda.org/conda-forge/noarch/wheel-0.43.0-pyhd8ed1ab_1.conda#0b5293a157c2b5cd513dd1b03d8d3aae -https://conda.anaconda.org/bioconda/linux-64/htslib-1.20-h81da01d_0.tar.bz2#1084947eefd2bbe9c1f84ca24061a9d5 -https://conda.anaconda.org/conda-forge/linux-64/libcblas-3.9.0-22_linux64_openblas.conda#4b31699e0ec5de64d5896e580389c9a1 +https://conda.anaconda.org/bioconda/linux-64/htslib-1.20-h5efdd21_2.tar.bz2#f0923cdb85b44dc77bdead8018645ea9 +https://conda.anaconda.org/conda-forge/linux-64/libcblas-3.9.0-23_linux64_openblas.conda#eede29b40efa878cbe5bdcb767e97310 https://conda.anaconda.org/conda-forge/noarch/pip-24.0-pyhd8ed1ab_0.conda#f586ac1e56c8638b64f9c8122a7b8a67 https://conda.anaconda.org/conda-forge/linux-64/gsl-2.7-he838d99_0.tar.bz2#fec079ba39c9cca093bf4c00001825de -https://conda.anaconda.org/bioconda/linux-64/samtools-1.20-h50ea8bc_0.tar.bz2#7b3b1d0feea64e7e211ae24e7cd126d8 -https://conda.anaconda.org/bioconda/linux-64/bcftools-1.20-h8b25389_0.tar.bz2#227ba3d820ac2f171b2ee20eb780cbac +https://conda.anaconda.org/bioconda/linux-64/samtools-1.20-h50ea8bc_1.tar.bz2#1a4c52f8079fea1b18b3e4bd329bab3a +https://conda.anaconda.org/bioconda/linux-64/bcftools-1.20-h8b25389_1.tar.bz2#7dea9d0b49ecf4a553472add3d297729 https://conda.anaconda.org/bioconda/linux-64/tabixpp-1.1.2-h27d5293_2.tar.bz2#7feba890b84ecc438f13cc88deb3e7da https://conda.anaconda.org/bioconda/linux-64/vcflib-1.0.9-hdcf5f25_6.tar.bz2#67a6e1c98e071c43b3c5ecf0ce6b1e63 https://conda.anaconda.org/bioconda/linux-64/freebayes-1.3.7-h6a68c12_2.tar.bz2#4eea99723233077c5a55b9c243e58883 diff --git a/bio/freebayes/environment.yaml b/bio/freebayes/environment.yaml index 5313ad3820e..421e89b68d2 100644 --- a/bio/freebayes/environment.yaml +++ b/bio/freebayes/environment.yaml @@ -7,7 +7,7 @@ dependencies: - bcftools =1.20 - vcflib =1.0.9 - htslib =1.20 - - parallel =20240522 + - parallel =20240722 - bedtools =2.31.1 - sed =4.8 - snakemake-wrapper-utils =0.6.2 From f9d678d51e1e81e1226f87432b98b510cd70901b Mon Sep 17 00:00:00 2001 From: "snakedeploy-bot[bot]" <115615832+snakedeploy-bot[bot]@users.noreply.github.com> Date: Fri, 26 Jul 2024 03:10:44 +0000 Subject: [PATCH 15/62] perf: autobump bio/fgbio/setmateinformation (#3088) Automatic bump of bio/fgbio/setmateinformation. --------- Co-authored-by: snakedeploy-bot[bot] <115615832+snakedeploy-bot[bot]@users.noreply.github.com> --- .../environment.linux-64.pin.txt | 174 +++++++++--------- bio/fgbio/setmateinformation/environment.yaml | 2 +- 2 files changed, 89 insertions(+), 87 deletions(-) diff --git a/bio/fgbio/setmateinformation/environment.linux-64.pin.txt b/bio/fgbio/setmateinformation/environment.linux-64.pin.txt index b437a3e2157..226bb2965fd 100644 --- a/bio/fgbio/setmateinformation/environment.linux-64.pin.txt +++ b/bio/fgbio/setmateinformation/environment.linux-64.pin.txt @@ -4,51 +4,46 @@ @EXPLICIT https://conda.anaconda.org/conda-forge/linux-64/_libgcc_mutex-0.1-conda_forge.tar.bz2#d7c89558ba9fa0495403155b64376d81 https://conda.anaconda.org/conda-forge/noarch/_r-mutex-1.0.1-anacondar_1.tar.bz2#19f9db5f4f1b7f5ef5f6d67207f25f38 -https://conda.anaconda.org/conda-forge/linux-64/ca-certificates-2024.2.2-hbcca054_0.conda#2f4327a1cbe7f022401b236e915a5fef +https://conda.anaconda.org/conda-forge/noarch/_sysroot_linux-64_curr_repodata_hack-3-h69a702a_16.conda#1c005af0c6ff22814b7c52ee448d4bea +https://conda.anaconda.org/conda-forge/linux-64/ca-certificates-2024.7.4-hbcca054_0.conda#23ab7665c5f63cfb9f1f6195256daac6 https://conda.anaconda.org/conda-forge/noarch/font-ttf-dejavu-sans-mono-2.37-hab24e00_0.tar.bz2#0c96522c6bdaed4b1566d11387caaf45 https://conda.anaconda.org/conda-forge/noarch/font-ttf-inconsolata-3.000-h77eed37_0.tar.bz2#34893075a5c9e55cdafac56607368fc6 https://conda.anaconda.org/conda-forge/noarch/font-ttf-source-code-pro-2.038-h77eed37_0.tar.bz2#4d59c254e01d9cde7957100457e2d5fb -https://conda.anaconda.org/conda-forge/noarch/font-ttf-ubuntu-0.83-h77eed37_1.conda#6185f640c43843e5ad6fd1c5372c3f80 -https://conda.anaconda.org/conda-forge/noarch/kernel-headers_linux-64-2.6.32-he073ed8_17.conda#d731b543793afc0433c4fd593e693fce -https://conda.anaconda.org/conda-forge/linux-64/ld_impl_linux-64-2.40-h41732ed_0.conda#7aca3059a1729aa76c597603f10b0dd3 -https://conda.anaconda.org/conda-forge/noarch/libgcc-devel_linux-64-13.2.0-ha9c7c90_105.conda#3bc29a967fee57e193ce51f51c598bca -https://conda.anaconda.org/conda-forge/noarch/libstdcxx-devel_linux-64-13.2.0-ha9c7c90_105.conda#66383205c2e1bdf013df52fa9e3e6763 -https://conda.anaconda.org/conda-forge/linux-64/libstdcxx-ng-13.2.0-h7e041cc_5.conda#f6f6600d18a4047b54f803cf708b868a +https://conda.anaconda.org/conda-forge/noarch/font-ttf-ubuntu-0.83-h77eed37_2.conda#cbbe59391138ea5ad3658c76912e147f +https://conda.anaconda.org/conda-forge/linux-64/ld_impl_linux-64-2.40-hf3520f5_7.conda#b80f2f396ca2c28b8c14c437a4ed1e74 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-https://conda.anaconda.org/conda-forge/noarch/r-viridislite-0.4.2-r43hc72bb7e_1.conda#307f6c8262afed91d2999568e2268ed6 -https://conda.anaconda.org/conda-forge/noarch/r-withr-3.0.0-r43hc72bb7e_0.conda#7380a50d9daae38b40777f7630b8c3ba -https://conda.anaconda.org/conda-forge/linux-64/r-ellipsis-0.3.2-r43h57805ef_2.conda#10c5892991072cfa3a61489d2ac6ad66 -https://conda.anaconda.org/conda-forge/noarch/r-lifecycle-1.0.4-r43hc72bb7e_0.conda#291d2fb68ea1b181644b40d6743ae000 -https://conda.anaconda.org/conda-forge/linux-64/r-matrix-1.6_5-r43h316c678_0.conda#8146ef1b3c54e1a484822085d39357b0 -https://conda.anaconda.org/conda-forge/noarch/r-munsell-0.5.0-r43hc72bb7e_1006.conda#22f529a11473af44bbe5d481bef9008d -https://conda.anaconda.org/conda-forge/linux-64/r-nlme-3.1_164-r43h61816a4_0.conda#7f44f44332abf00df114c685b1d6054c -https://conda.anaconda.org/conda-forge/noarch/r-gtable-0.3.4-r43hc72bb7e_0.conda#11c5e5e3bd2b41005177c28c1ba46dc3 -https://conda.anaconda.org/conda-forge/linux-64/r-mgcv-1.9_1-r43h316c678_0.conda#c73d9ed0dc98182d712cbea33a3e5d59 -https://conda.anaconda.org/conda-forge/noarch/r-scales-1.3.0-r43hc72bb7e_0.conda#508360956e18c2b0cc18968cdb786c78 -https://conda.anaconda.org/conda-forge/linux-64/r-vctrs-0.6.5-r43ha503ecb_0.conda#e398bd0451e6350a876a8561f8e90682 -https://conda.anaconda.org/conda-forge/noarch/r-pillar-1.9.0-r43hc72bb7e_1.conda#7cff01456566a69381d3907d520c10b2 -https://conda.anaconda.org/conda-forge/linux-64/r-tibble-3.2.1-r43h57805ef_2.conda#afa7d3f21fbc5a2fbaa48cb9bacb7bce -https://conda.anaconda.org/conda-forge/noarch/r-ggplot2-3.5.0-r43hc72bb7e_0.conda#f5fc39155735cfc3c0c680620301dfa8 -https://conda.anaconda.org/bioconda/noarch/fgbio-2.2.1-hdfd78af_0.tar.bz2#896491578e7847a8a0d57cca2c698bd8 +https://conda.anaconda.org/conda-forge/linux-64/gsl-2.7-he838d99_0.tar.bz2#fec079ba39c9cca093bf4c00001825de +https://conda.anaconda.org/conda-forge/linux-64/harfbuzz-9.0.0-hda332d3_1.conda#76b32dcf243444aea9c6b804bcfa40b8 +https://conda.anaconda.org/conda-forge/linux-64/xorg-libxtst-1.2.4-h4bc722e_0.conda#4561491e71d04bfe58d4f0ce5329656e +https://conda.anaconda.org/conda-forge/linux-64/openjdk-22.0.1-h8651b0f_1.conda#672153e7c3d4f70bc65993f3ee513768 +https://conda.anaconda.org/conda-forge/linux-64/pango-1.54.0-h4c5309f_1.conda#7df02e445367703cd87a574046e3a6f0 +https://conda.anaconda.org/conda-forge/linux-64/r-base-4.4.1-h745b8e0_13.conda#62d2555c44e35394e9eafaaaa7393e2c +https://conda.anaconda.org/conda-forge/linux-64/r-cli-3.6.3-r44h0d4f4ea_1.conda#4f07a3d62def16d73303c8435e17a62e +https://conda.anaconda.org/conda-forge/linux-64/r-colorspace-2.1_0-r44hb1dbf0f_2.conda#b48997750aea2a8ed02e80cd94310c2d +https://conda.anaconda.org/conda-forge/noarch/r-crayon-1.5.3-r44hc72bb7e_1.conda#89626d77a94256b8304bb8fc33d3364c +https://conda.anaconda.org/conda-forge/linux-64/r-fansi-1.0.6-r44hb1dbf0f_1.conda#c4c0d4b82b54899c61c6f3e09b1bcc5c +https://conda.anaconda.org/conda-forge/linux-64/r-farver-2.1.2-r44ha18555a_1.conda#c2cf909117c44802caf096dd8ba8038e +https://conda.anaconda.org/conda-forge/linux-64/r-glue-1.7.0-r44hb1dbf0f_1.conda#353c728f5a70cb0c530c01c47cc6bb66 +https://conda.anaconda.org/conda-forge/linux-64/r-isoband-0.2.7-r44ha18555a_3.conda#4745fadbe3c521e46d9c9b39148ac3c7 +https://conda.anaconda.org/conda-forge/noarch/r-labeling-0.4.3-r44hc72bb7e_1.conda#49f2c043dfb8f5003dea36ae39ca1103 +https://conda.anaconda.org/conda-forge/linux-64/r-lattice-0.22_6-r44hb1dbf0f_1.conda#507b46f5005deff049c88453165b30d3 +https://conda.anaconda.org/conda-forge/linux-64/r-magrittr-2.0.3-r44hb1dbf0f_3.conda#a53562b6400cbbf0323fb97881ba61b3 +https://conda.anaconda.org/conda-forge/linux-64/r-mass-7.3_60.0.1-r44hb1dbf0f_1.conda#17c05547f2f9a5c340d1c9d20483bfe4 +https://conda.anaconda.org/conda-forge/noarch/r-pkgconfig-2.0.3-r44hc72bb7e_4.conda#17d36e686fb918637ca43fc4c036549e +https://conda.anaconda.org/conda-forge/noarch/r-r6-2.5.1-r44hc72bb7e_3.conda#d3f65826d814916e29288c4413109011 +https://conda.anaconda.org/conda-forge/noarch/r-rcolorbrewer-1.1_3-r44h785f33e_3.conda#1f23714459a514fb7597fa15671d3cc6 +https://conda.anaconda.org/conda-forge/linux-64/r-rlang-1.1.4-r44ha18555a_1.conda#e090c65a64aee15334bb8a5415c8be69 +https://conda.anaconda.org/conda-forge/linux-64/r-utf8-1.2.4-r44hb1dbf0f_1.conda#11331e679a538de7c85ced8d293394a2 +https://conda.anaconda.org/conda-forge/noarch/r-viridislite-0.4.2-r44hc72bb7e_2.conda#7cf7a6974364e6853f1a06554dfaa3e5 +https://conda.anaconda.org/conda-forge/noarch/r-withr-3.0.0-r44hc72bb7e_1.conda#31b38d8ae1db462b21090df6182146d9 +https://conda.anaconda.org/conda-forge/linux-64/r-ellipsis-0.3.2-r44hb1dbf0f_3.conda#a96cb6b4b61efd45ffe47019af5eb879 +https://conda.anaconda.org/conda-forge/noarch/r-lifecycle-1.0.4-r44hc72bb7e_1.conda#66d0ba7c05d0abfa11d126ba8e2907aa +https://conda.anaconda.org/conda-forge/linux-64/r-matrix-1.6_5-r44he966344_1.conda#bbcb8fe02b64b3b69bf078f2020f7446 +https://conda.anaconda.org/conda-forge/noarch/r-munsell-0.5.1-r44hc72bb7e_1.conda#871dfde2639a8fdfe210eea7c59fd1e8 +https://conda.anaconda.org/conda-forge/linux-64/r-nlme-3.1_165-r44hbcb9c34_1.conda#b579f3ffba329dd5b46bddb429a8aa2e +https://conda.anaconda.org/conda-forge/noarch/r-gtable-0.3.5-r44hc72bb7e_1.conda#c3040db0b657a19a071ed472d24a204d +https://conda.anaconda.org/conda-forge/linux-64/r-mgcv-1.9_1-r44h0d28552_1.conda#3bd992bc484600de3b23809fb76eb7bb +https://conda.anaconda.org/conda-forge/noarch/r-scales-1.3.0-r44hc72bb7e_1.conda#31cda9180dde0613a04a020771eb2d09 +https://conda.anaconda.org/conda-forge/linux-64/r-vctrs-0.6.5-r44h0d4f4ea_1.conda#399bc7872bdb40b5531d887858253e76 +https://conda.anaconda.org/conda-forge/noarch/r-pillar-1.9.0-r44hc72bb7e_2.conda#3ec6418c9af0a90d4513cadfe0ef863a +https://conda.anaconda.org/conda-forge/linux-64/r-tibble-3.2.1-r44hdb488b9_3.conda#03203ac70558ba5bb836d1cb641f1b87 +https://conda.anaconda.org/conda-forge/noarch/r-ggplot2-3.5.1-r44hc72bb7e_1.conda#c6209f7de229696ebd0086e7c27a02ac +https://conda.anaconda.org/bioconda/noarch/fgbio-2.3.0-hdfd78af_0.tar.bz2#2b0378bb6f00f8fb837886a807603e27 diff --git a/bio/fgbio/setmateinformation/environment.yaml b/bio/fgbio/setmateinformation/environment.yaml index f1f997b6554..997b5b62cfb 100644 --- a/bio/fgbio/setmateinformation/environment.yaml +++ b/bio/fgbio/setmateinformation/environment.yaml @@ -3,4 +3,4 @@ channels: - bioconda - nodefaults dependencies: - - fgbio =2.2.1 + - fgbio =2.3.0 From 5de22930fe0f9fd6e8350bea5000a2c9b50d10d7 Mon Sep 17 00:00:00 2001 From: "snakedeploy-bot[bot]" <115615832+snakedeploy-bot[bot]@users.noreply.github.com> Date: Fri, 26 Jul 2024 03:22:49 +0000 Subject: [PATCH 16/62] perf: autobump bio/gdc-api/bam-slicing (#3089) Automatic bump of bio/gdc-api/bam-slicing. --------- Co-authored-by: snakedeploy-bot[bot] <115615832+snakedeploy-bot[bot]@users.noreply.github.com> --- .../bam-slicing/environment.linux-64.pin.txt | 20 +++++++++---------- bio/gdc-api/bam-slicing/environment.yaml | 2 +- 2 files changed, 11 insertions(+), 11 deletions(-) diff --git a/bio/gdc-api/bam-slicing/environment.linux-64.pin.txt b/bio/gdc-api/bam-slicing/environment.linux-64.pin.txt index 170a097095b..bb2c4eb472f 100644 --- a/bio/gdc-api/bam-slicing/environment.linux-64.pin.txt +++ b/bio/gdc-api/bam-slicing/environment.linux-64.pin.txt @@ -3,21 +3,21 @@ # platform: linux-64 @EXPLICIT https://conda.anaconda.org/conda-forge/linux-64/_libgcc_mutex-0.1-conda_forge.tar.bz2#d7c89558ba9fa0495403155b64376d81 -https://conda.anaconda.org/conda-forge/linux-64/ca-certificates-2024.2.2-hbcca054_0.conda#2f4327a1cbe7f022401b236e915a5fef -https://conda.anaconda.org/conda-forge/linux-64/libstdcxx-ng-13.2.0-hc0a3c3a_7.conda#53ebd4c833fa01cb2c6353e99f905406 -https://conda.anaconda.org/conda-forge/linux-64/libgomp-13.2.0-h77fa898_7.conda#abf3fec87c2563697defa759dec3d639 +https://conda.anaconda.org/conda-forge/linux-64/ca-certificates-2024.7.4-hbcca054_0.conda#23ab7665c5f63cfb9f1f6195256daac6 +https://conda.anaconda.org/conda-forge/linux-64/libgomp-14.1.0-h77fa898_0.conda#ae061a5ed5f05818acdf9adab72c146d https://conda.anaconda.org/conda-forge/linux-64/_openmp_mutex-4.5-2_gnu.tar.bz2#73aaf86a425cc6e73fcf236a5a46396d -https://conda.anaconda.org/conda-forge/linux-64/libgcc-ng-13.2.0-h77fa898_7.conda#72ec1b1b04c4d15d4204ece1ecea5978 -https://conda.anaconda.org/conda-forge/linux-64/c-ares-1.28.1-hd590300_0.conda#dcde58ff9a1f30b0037a2315d1846d1f +https://conda.anaconda.org/conda-forge/linux-64/libgcc-ng-14.1.0-h77fa898_0.conda#ca0fad6a41ddaef54a153b78eccb5037 +https://conda.anaconda.org/conda-forge/linux-64/c-ares-1.32.3-h4bc722e_0.conda#7624e34ee6baebfc80d67bac76cc9d9d https://conda.anaconda.org/conda-forge/linux-64/keyutils-1.6.1-h166bdaf_0.tar.bz2#30186d27e2c9fa62b45fb1476b7200e3 https://conda.anaconda.org/conda-forge/linux-64/libev-4.33-hd590300_2.conda#172bf1cd1ff8629f2b1179945ed45055 -https://conda.anaconda.org/conda-forge/linux-64/libzlib-1.2.13-hd590300_5.conda#f36c115f1ee199da648e0597ec2047ad +https://conda.anaconda.org/conda-forge/linux-64/libstdcxx-ng-14.1.0-hc0a3c3a_0.conda#1cb187a157136398ddbaae90713e2498 +https://conda.anaconda.org/conda-forge/linux-64/libzlib-1.3.1-h4ab18f5_1.conda#57d7dc60e9325e3de37ff8dffd18e814 https://conda.anaconda.org/conda-forge/linux-64/ncurses-6.5-h59595ed_0.conda#fcea371545eda051b6deafb24889fc69 -https://conda.anaconda.org/conda-forge/linux-64/openssl-3.3.0-h4ab18f5_3.conda#12ea6d0d4ed54530eaed18e4835c1f7c +https://conda.anaconda.org/conda-forge/linux-64/openssl-3.3.1-h4bc722e_2.conda#e1b454497f9f7c1147fdde4b53f1b512 https://conda.anaconda.org/conda-forge/linux-64/libedit-3.1.20191231-he28a2e2_2.tar.bz2#4d331e44109e3f0e19b4cb8f9b82f3e1 https://conda.anaconda.org/conda-forge/linux-64/libnghttp2-1.58.0-h47da74e_1.conda#700ac6ea6d53d5510591c4344d5c989a https://conda.anaconda.org/conda-forge/linux-64/libssh2-1.11.0-h0841786_0.conda#1f5a58e686b13bcfde88b93f547d23fe https://conda.anaconda.org/conda-forge/linux-64/zstd-1.5.6-ha6fb4c9_0.conda#4d056880988120e29d75bfff282e0f45 -https://conda.anaconda.org/conda-forge/linux-64/krb5-1.21.2-h659d440_0.conda#cd95826dbd331ed1be26bdf401432844 -https://conda.anaconda.org/conda-forge/linux-64/libcurl-8.8.0-hca28451_0.conda#f21c27f076a07907e70c49bb57bd0f20 -https://conda.anaconda.org/conda-forge/linux-64/curl-8.8.0-he654da7_0.conda#042341d8b9ba4ee7f2722b81fae9f0ad +https://conda.anaconda.org/conda-forge/linux-64/krb5-1.21.3-h659f571_0.conda#3f43953b7d3fb3aaa1d0d0723d91e368 +https://conda.anaconda.org/conda-forge/linux-64/libcurl-8.9.0-hdb1bdb2_0.conda#5badfbdb2688d8aaca7bd3c98d557b97 +https://conda.anaconda.org/conda-forge/linux-64/curl-8.9.0-h18eb788_0.conda#cb385c8a955ad49c3342b23cd1a26c11 diff --git a/bio/gdc-api/bam-slicing/environment.yaml b/bio/gdc-api/bam-slicing/environment.yaml index 59fd406b09e..0371dd78aaf 100644 --- a/bio/gdc-api/bam-slicing/environment.yaml +++ b/bio/gdc-api/bam-slicing/environment.yaml @@ -2,4 +2,4 @@ channels: - conda-forge - nodefaults dependencies: - - curl =8.8.0 + - curl =8.9.0 From 9e1cc9914508fe883d4bfca064282b36fc1399f5 Mon Sep 17 00:00:00 2001 From: "snakedeploy-bot[bot]" <115615832+snakedeploy-bot[bot]@users.noreply.github.com> Date: Fri, 26 Jul 2024 04:30:23 +0000 Subject: [PATCH 17/62] perf: autobump bio/nonpareil/infer (#3092) Automatic bump of bio/nonpareil/infer. --------- Co-authored-by: snakedeploy-bot[bot] <115615832+snakedeploy-bot[bot]@users.noreply.github.com> --- .../infer/environment.linux-64.pin.txt | 37 ++++++++++--------- bio/nonpareil/infer/environment.yaml | 2 +- 2 files changed, 21 insertions(+), 18 deletions(-) diff --git a/bio/nonpareil/infer/environment.linux-64.pin.txt b/bio/nonpareil/infer/environment.linux-64.pin.txt index 2a58147cf1f..c627672f1db 100644 --- a/bio/nonpareil/infer/environment.linux-64.pin.txt +++ b/bio/nonpareil/infer/environment.linux-64.pin.txt @@ -4,7 +4,7 @@ @EXPLICIT https://conda.anaconda.org/conda-forge/linux-64/_libgcc_mutex-0.1-conda_forge.tar.bz2#d7c89558ba9fa0495403155b64376d81 https://conda.anaconda.org/conda-forge/noarch/_r-mutex-1.0.1-anacondar_1.tar.bz2#19f9db5f4f1b7f5ef5f6d67207f25f38 -https://conda.anaconda.org/conda-forge/noarch/_sysroot_linux-64_curr_repodata_hack-3-h69a702a_15.conda#662e1be2f85cef241c8edeced147aec8 +https://conda.anaconda.org/conda-forge/noarch/_sysroot_linux-64_curr_repodata_hack-3-h69a702a_16.conda#1c005af0c6ff22814b7c52ee448d4bea https://conda.anaconda.org/conda-forge/linux-64/ca-certificates-2024.7.4-hbcca054_0.conda#23ab7665c5f63cfb9f1f6195256daac6 https://conda.anaconda.org/conda-forge/noarch/font-ttf-dejavu-sans-mono-2.37-hab24e00_0.tar.bz2#0c96522c6bdaed4b1566d11387caaf45 https://conda.anaconda.org/conda-forge/noarch/font-ttf-inconsolata-3.000-h77eed37_0.tar.bz2#34893075a5c9e55cdafac56607368fc6 @@ -15,15 +15,15 @@ https://conda.anaconda.org/conda-forge/noarch/libgcc-devel_linux-64-14.1.0-h5d3d https://conda.anaconda.org/conda-forge/noarch/libstdcxx-devel_linux-64-14.1.0-h5d3d1c9_100.conda#cedc62fd8c4cf28f23d3cd5db7839e99 https://conda.anaconda.org/conda-forge/noarch/tzdata-2024a-h0c530f3_0.conda#161081fc7cec0bfda0d86d7cb595f8d8 https://conda.anaconda.org/conda-forge/noarch/fonts-conda-forge-1-0.tar.bz2#f766549260d6815b0c52253f1fb1bb29 -https://conda.anaconda.org/conda-forge/noarch/kernel-headers_linux-64-3.10.0-h4a8ded7_15.conda#38d8b37108f7be26dc816bc37c3ced39 +https://conda.anaconda.org/conda-forge/noarch/kernel-headers_linux-64-3.10.0-h4a8ded7_16.conda#ff7f38675b226cfb855aebfc32a13e31 https://conda.anaconda.org/conda-forge/linux-64/libgomp-14.1.0-h77fa898_0.conda#ae061a5ed5f05818acdf9adab72c146d https://conda.anaconda.org/conda-forge/linux-64/_openmp_mutex-4.5-2_gnu.tar.bz2#73aaf86a425cc6e73fcf236a5a46396d https://conda.anaconda.org/conda-forge/noarch/fonts-conda-ecosystem-1-0.tar.bz2#fee5683a3f04bd15cbd8318b096a27ab -https://conda.anaconda.org/conda-forge/noarch/sysroot_linux-64-2.17-h4a8ded7_15.conda#bf901c816d5671f9ae64e0c6e1c589ad +https://conda.anaconda.org/conda-forge/noarch/sysroot_linux-64-2.17-h4a8ded7_16.conda#223fe8a3ff6d5e78484a9d58eb34d055 https://conda.anaconda.org/conda-forge/linux-64/binutils_impl_linux-64-2.40-ha1999f0_7.conda#3f840c7ed70a96b5ebde8044b2f36f32 https://conda.anaconda.org/conda-forge/linux-64/libgcc-ng-14.1.0-h77fa898_0.conda#ca0fad6a41ddaef54a153b78eccb5037 -https://conda.anaconda.org/conda-forge/linux-64/bzip2-1.0.8-hd590300_5.conda#69b8b6202a07720f448be700e300ccf4 -https://conda.anaconda.org/conda-forge/linux-64/c-ares-1.28.1-hd590300_0.conda#dcde58ff9a1f30b0037a2315d1846d1f +https://conda.anaconda.org/conda-forge/linux-64/bzip2-1.0.8-h4bc722e_7.conda#62ee74e96c5ebb0af99386de58cf9553 +https://conda.anaconda.org/conda-forge/linux-64/c-ares-1.32.3-h4bc722e_0.conda#7624e34ee6baebfc80d67bac76cc9d9d https://conda.anaconda.org/conda-forge/linux-64/fribidi-1.0.10-h36c2ea0_0.tar.bz2#ac7bc6a654f8f41b352b38f4051135f8 https://conda.anaconda.org/conda-forge/linux-64/keyutils-1.6.1-h166bdaf_0.tar.bz2#30186d27e2c9fa62b45fb1476b7200e3 https://conda.anaconda.org/conda-forge/linux-64/libdeflate-1.20-hd590300_0.conda#8e88f9389f1165d7c0936fe40d9a9a79 @@ -41,7 +41,7 @@ https://conda.anaconda.org/conda-forge/linux-64/libxcrypt-4.4.36-hd590300_1.cond https://conda.anaconda.org/conda-forge/linux-64/libzlib-1.3.1-h4ab18f5_1.conda#57d7dc60e9325e3de37ff8dffd18e814 https://conda.anaconda.org/conda-forge/linux-64/make-4.3-hd18ef5c_1.tar.bz2#4049ebfd3190b580dffe76daed26155a https://conda.anaconda.org/conda-forge/linux-64/ncurses-6.5-h59595ed_0.conda#fcea371545eda051b6deafb24889fc69 -https://conda.anaconda.org/conda-forge/linux-64/openssl-3.3.1-h4ab18f5_1.conda#b1e9d076f14e8d776213fd5047b4c3d9 +https://conda.anaconda.org/conda-forge/linux-64/openssl-3.3.1-h4bc722e_2.conda#e1b454497f9f7c1147fdde4b53f1b512 https://conda.anaconda.org/conda-forge/linux-64/pthread-stubs-0.4-h36c2ea0_1001.tar.bz2#22dad4df6e8630e8dff2428f6f6a7036 https://conda.anaconda.org/conda-forge/linux-64/sed-4.8-he412f7d_0.tar.bz2#7362f0042e95681f5d371c46c83ebd08 https://conda.anaconda.org/conda-forge/linux-64/xorg-kbproto-1.0.7-h7f98852_1002.tar.bz2#4b230e8381279d76131116660f5a241a @@ -54,7 +54,7 @@ https://conda.anaconda.org/conda-forge/linux-64/xorg-xproto-7.0.31-h7f98852_1007 https://conda.anaconda.org/conda-forge/linux-64/xz-5.2.6-h166bdaf_0.tar.bz2#2161070d867d1b1204ea749c8eec4ef0 https://conda.anaconda.org/conda-forge/linux-64/expat-2.6.2-h59595ed_0.conda#53fb86322bdb89496d7579fe3f02fd61 https://conda.anaconda.org/conda-forge/linux-64/graphite2-1.3.13-h59595ed_1003.conda#f87c7b7c2cb45f323ffbce941c78ab7c -https://conda.anaconda.org/conda-forge/linux-64/icu-73.2-h59595ed_0.conda#cc47e1facc155f91abd89b11e48e72ff +https://conda.anaconda.org/conda-forge/linux-64/icu-75.1-he02047a_0.conda#8b189310083baabfb622af68fd9d3ae3 https://conda.anaconda.org/conda-forge/linux-64/lerc-4.0.0-h27087fc_0.tar.bz2#76bbff344f0134279f225174e9064c8f https://conda.anaconda.org/conda-forge/linux-64/libedit-3.1.20191231-he28a2e2_2.tar.bz2#4d331e44109e3f0e19b4cb8f9b82f3e1 https://conda.anaconda.org/conda-forge/linux-64/libgfortran-ng-14.1.0-h69a702a_0.conda#f4ca84fbd6d06b0a052fb2d5b96dde41 @@ -86,21 +86,24 @@ https://conda.anaconda.org/conda-forge/linux-64/xorg-libx11-1.8.9-hb711507_1.con https://conda.anaconda.org/conda-forge/linux-64/fontconfig-2.14.2-h14ed4e7_0.conda#0f69b688f52ff6da70bccb7ff7001d1d https://conda.anaconda.org/conda-forge/linux-64/gfortran_impl_linux-64-14.1.0-he4a1faa_0.conda#a9ce7cd0848a93a8df88c1fc0ac84d9d https://conda.anaconda.org/conda-forge/linux-64/gxx_impl_linux-64-14.1.0-h2879b86_0.conda#47d6de998d7a285b98b60bce2fecb54b -https://conda.anaconda.org/conda-forge/linux-64/libblas-3.9.0-22_linux64_openblas.conda#1a2a0cd3153464fee6646f3dd6dad9b8 -https://conda.anaconda.org/conda-forge/linux-64/libcurl-8.8.0-hca28451_1.conda#b8afb3e3cb3423cc445cf611ab95fdb0 -https://conda.anaconda.org/conda-forge/noarch/setuptools-70.2.0-pyhd8ed1ab_0.conda#10170a48c48cfe65eab923f76f982087 +https://conda.anaconda.org/conda-forge/linux-64/libblas-3.9.0-23_linux64_openblas.conda#96c8450a40aa2b9733073a9460de972c +https://conda.anaconda.org/conda-forge/linux-64/libcurl-8.9.0-hdb1bdb2_0.conda#5badfbdb2688d8aaca7bd3c98d557b97 +https://conda.anaconda.org/conda-forge/noarch/setuptools-71.0.4-pyhd8ed1ab_0.conda#ee78ac9c720d0d02fcfd420866b82ab1 https://conda.anaconda.org/bioconda/noarch/snakemake-wrapper-utils-0.6.2-pyhdfd78af_0.tar.bz2#fd8759bbd04116eace828c4fab906096 https://conda.anaconda.org/conda-forge/noarch/wheel-0.43.0-pyhd8ed1ab_1.conda#0b5293a157c2b5cd513dd1b03d8d3aae https://conda.anaconda.org/conda-forge/linux-64/xorg-libxext-1.3.4-h0b41bf4_2.conda#82b6df12252e6f32402b96dacc656fec https://conda.anaconda.org/conda-forge/linux-64/xorg-libxrender-0.9.11-hd590300_0.conda#ed67c36f215b310412b2af935bf3e530 https://conda.anaconda.org/conda-forge/linux-64/xorg-libxt-1.3.0-hd590300_1.conda#ae92aab42726eb29d16488924f7312cb -https://conda.anaconda.org/conda-forge/linux-64/cairo-1.18.0-hbb29018_2.conda#b6d90276c5aee9b4407dd94eb0cd40a8 -https://conda.anaconda.org/conda-forge/linux-64/curl-8.8.0-he654da7_1.conda#78678b2ddfd9bd7c7861b8d2e3b7473b -https://conda.anaconda.org/conda-forge/linux-64/libcblas-3.9.0-22_linux64_openblas.conda#4b31699e0ec5de64d5896e580389c9a1 -https://conda.anaconda.org/conda-forge/linux-64/liblapack-3.9.0-22_linux64_openblas.conda#b083767b6c877e24ee597d93b87ab838 +https://conda.anaconda.org/conda-forge/linux-64/cairo-1.18.0-hebfffa5_3.conda#fceaedf1cdbcb02df9699a0d9b005292 +https://conda.anaconda.org/conda-forge/linux-64/curl-8.9.0-h18eb788_0.conda#cb385c8a955ad49c3342b23cd1a26c11 +https://conda.anaconda.org/conda-forge/linux-64/libcblas-3.9.0-23_linux64_openblas.conda#eede29b40efa878cbe5bdcb767e97310 +https://conda.anaconda.org/conda-forge/linux-64/liblapack-3.9.0-23_linux64_openblas.conda#2af0879961951987e464722fd00ec1e0 https://conda.anaconda.org/conda-forge/noarch/pip-24.0-pyhd8ed1ab_0.conda#f586ac1e56c8638b64f9c8122a7b8a67 https://conda.anaconda.org/conda-forge/linux-64/gsl-2.7-he838d99_0.tar.bz2#fec079ba39c9cca093bf4c00001825de -https://conda.anaconda.org/conda-forge/linux-64/harfbuzz-9.0.0-hfac3d4d_0.conda#c7b47c64af53e8ecee01d101eeab2342 +https://conda.anaconda.org/conda-forge/linux-64/harfbuzz-9.0.0-hda332d3_1.conda#76b32dcf243444aea9c6b804bcfa40b8 https://conda.anaconda.org/conda-forge/linux-64/pango-1.54.0-h4c5309f_1.conda#7df02e445367703cd87a574046e3a6f0 -https://conda.anaconda.org/conda-forge/linux-64/r-base-4.3.3-he2d9a6e_10.conda#f29b857679e49c026984531249e542fd -https://conda.anaconda.org/bioconda/linux-64/nonpareil-3.5.4-r43hdcf5f25_0.tar.bz2#f2ab75cfbe5fa7cc418670ab5becee30 +https://conda.anaconda.org/conda-forge/linux-64/r-base-4.3.3-h9967228_12.conda#88e0b778762c6ffa75241d0f34cfa94e +https://conda.anaconda.org/conda-forge/noarch/r-getopt-1.20.4-r43ha770c72_1.conda#cf6793c369dbc7ef63d9c1bc9b186615 +https://conda.anaconda.org/conda-forge/linux-64/r-jsonlite-1.8.8-r43hb1dbf0f_1.conda#eb4377db2a26436aed657474aad972aa +https://conda.anaconda.org/conda-forge/noarch/r-optparse-1.7.5-r43hc72bb7e_1.conda#ae32080aac0f74e73e7cd6e774db1c73 +https://conda.anaconda.org/bioconda/linux-64/nonpareil-3.5.5-r43hdcf5f25_0.tar.bz2#3aa5e80948e3cd9a9dedbf5a201cc66d diff --git a/bio/nonpareil/infer/environment.yaml b/bio/nonpareil/infer/environment.yaml index b9a0fa3406f..d9a39f601f4 100644 --- a/bio/nonpareil/infer/environment.yaml +++ b/bio/nonpareil/infer/environment.yaml @@ -3,7 +3,7 @@ channels: - bioconda - nodefaults dependencies: - - nonpareil =3.5.4 + - nonpareil =3.5.5 - pigz - pbzip2 - snakemake-wrapper-utils =0.6.2 From 4b465798b021e179830bc2ed980f4a5c194fcba2 Mon Sep 17 00:00:00 2001 From: "snakedeploy-bot[bot]" <115615832+snakedeploy-bot[bot]@users.noreply.github.com> Date: Fri, 26 Jul 2024 04:31:03 +0000 Subject: [PATCH 18/62] perf: autobump bio/nonpareil/plot (#3093) Automatic bump of bio/nonpareil/plot. --------- Co-authored-by: snakedeploy-bot[bot] <115615832+snakedeploy-bot[bot]@users.noreply.github.com> --- .../plot/environment.linux-64.pin.txt | 28 ++++++++++--------- bio/nonpareil/plot/environment.yaml | 2 +- 2 files changed, 16 insertions(+), 14 deletions(-) diff --git a/bio/nonpareil/plot/environment.linux-64.pin.txt b/bio/nonpareil/plot/environment.linux-64.pin.txt index 2c273f49e52..153ca511610 100644 --- a/bio/nonpareil/plot/environment.linux-64.pin.txt +++ b/bio/nonpareil/plot/environment.linux-64.pin.txt @@ -22,8 +22,8 @@ https://conda.anaconda.org/conda-forge/noarch/fonts-conda-ecosystem-1-0.tar.bz2# https://conda.anaconda.org/conda-forge/noarch/sysroot_linux-64-2.17-h4a8ded7_16.conda#223fe8a3ff6d5e78484a9d58eb34d055 https://conda.anaconda.org/conda-forge/linux-64/binutils_impl_linux-64-2.40-ha1999f0_7.conda#3f840c7ed70a96b5ebde8044b2f36f32 https://conda.anaconda.org/conda-forge/linux-64/libgcc-ng-14.1.0-h77fa898_0.conda#ca0fad6a41ddaef54a153b78eccb5037 -https://conda.anaconda.org/conda-forge/linux-64/bzip2-1.0.8-hd590300_5.conda#69b8b6202a07720f448be700e300ccf4 -https://conda.anaconda.org/conda-forge/linux-64/c-ares-1.32.0-h4ab18f5_0.conda#7f3a7d68b591fcace97c29c6af6d9d64 +https://conda.anaconda.org/conda-forge/linux-64/bzip2-1.0.8-h4bc722e_7.conda#62ee74e96c5ebb0af99386de58cf9553 +https://conda.anaconda.org/conda-forge/linux-64/c-ares-1.32.3-h4bc722e_0.conda#7624e34ee6baebfc80d67bac76cc9d9d https://conda.anaconda.org/conda-forge/linux-64/fribidi-1.0.10-h36c2ea0_0.tar.bz2#ac7bc6a654f8f41b352b38f4051135f8 https://conda.anaconda.org/conda-forge/linux-64/keyutils-1.6.1-h166bdaf_0.tar.bz2#30186d27e2c9fa62b45fb1476b7200e3 https://conda.anaconda.org/conda-forge/linux-64/libdeflate-1.20-hd590300_0.conda#8e88f9389f1165d7c0936fe40d9a9a79 @@ -39,7 +39,7 @@ https://conda.anaconda.org/conda-forge/linux-64/libwebp-base-1.4.0-hd590300_0.co https://conda.anaconda.org/conda-forge/linux-64/libzlib-1.3.1-h4ab18f5_1.conda#57d7dc60e9325e3de37ff8dffd18e814 https://conda.anaconda.org/conda-forge/linux-64/make-4.3-hd18ef5c_1.tar.bz2#4049ebfd3190b580dffe76daed26155a https://conda.anaconda.org/conda-forge/linux-64/ncurses-6.5-h59595ed_0.conda#fcea371545eda051b6deafb24889fc69 -https://conda.anaconda.org/conda-forge/linux-64/openssl-3.3.1-h4ab18f5_1.conda#b1e9d076f14e8d776213fd5047b4c3d9 +https://conda.anaconda.org/conda-forge/linux-64/openssl-3.3.1-h4bc722e_2.conda#e1b454497f9f7c1147fdde4b53f1b512 https://conda.anaconda.org/conda-forge/linux-64/pthread-stubs-0.4-h36c2ea0_1001.tar.bz2#22dad4df6e8630e8dff2428f6f6a7036 https://conda.anaconda.org/conda-forge/linux-64/sed-4.8-he412f7d_0.tar.bz2#7362f0042e95681f5d371c46c83ebd08 https://conda.anaconda.org/conda-forge/linux-64/xorg-kbproto-1.0.7-h7f98852_1002.tar.bz2#4b230e8381279d76131116660f5a241a @@ -52,7 +52,7 @@ https://conda.anaconda.org/conda-forge/linux-64/xorg-xproto-7.0.31-h7f98852_1007 https://conda.anaconda.org/conda-forge/linux-64/xz-5.2.6-h166bdaf_0.tar.bz2#2161070d867d1b1204ea749c8eec4ef0 https://conda.anaconda.org/conda-forge/linux-64/expat-2.6.2-h59595ed_0.conda#53fb86322bdb89496d7579fe3f02fd61 https://conda.anaconda.org/conda-forge/linux-64/graphite2-1.3.13-h59595ed_1003.conda#f87c7b7c2cb45f323ffbce941c78ab7c -https://conda.anaconda.org/conda-forge/linux-64/icu-73.2-h59595ed_0.conda#cc47e1facc155f91abd89b11e48e72ff +https://conda.anaconda.org/conda-forge/linux-64/icu-75.1-he02047a_0.conda#8b189310083baabfb622af68fd9d3ae3 https://conda.anaconda.org/conda-forge/linux-64/lerc-4.0.0-h27087fc_0.tar.bz2#76bbff344f0134279f225174e9064c8f https://conda.anaconda.org/conda-forge/linux-64/libedit-3.1.20191231-he28a2e2_2.tar.bz2#4d331e44109e3f0e19b4cb8f9b82f3e1 https://conda.anaconda.org/conda-forge/linux-64/libgfortran-ng-14.1.0-h69a702a_0.conda#f4ca84fbd6d06b0a052fb2d5b96dde41 @@ -80,18 +80,20 @@ https://conda.anaconda.org/conda-forge/linux-64/xorg-libx11-1.8.9-hb711507_1.con https://conda.anaconda.org/conda-forge/linux-64/fontconfig-2.14.2-h14ed4e7_0.conda#0f69b688f52ff6da70bccb7ff7001d1d https://conda.anaconda.org/conda-forge/linux-64/gfortran_impl_linux-64-14.1.0-he4a1faa_0.conda#a9ce7cd0848a93a8df88c1fc0ac84d9d https://conda.anaconda.org/conda-forge/linux-64/gxx_impl_linux-64-14.1.0-h2879b86_0.conda#47d6de998d7a285b98b60bce2fecb54b -https://conda.anaconda.org/conda-forge/linux-64/libblas-3.9.0-22_linux64_openblas.conda#1a2a0cd3153464fee6646f3dd6dad9b8 -https://conda.anaconda.org/conda-forge/linux-64/libcurl-8.8.0-hca28451_1.conda#b8afb3e3cb3423cc445cf611ab95fdb0 +https://conda.anaconda.org/conda-forge/linux-64/libblas-3.9.0-23_linux64_openblas.conda#96c8450a40aa2b9733073a9460de972c +https://conda.anaconda.org/conda-forge/linux-64/libcurl-8.9.0-hdb1bdb2_0.conda#5badfbdb2688d8aaca7bd3c98d557b97 https://conda.anaconda.org/conda-forge/linux-64/xorg-libxext-1.3.4-h0b41bf4_2.conda#82b6df12252e6f32402b96dacc656fec https://conda.anaconda.org/conda-forge/linux-64/xorg-libxrender-0.9.11-hd590300_0.conda#ed67c36f215b310412b2af935bf3e530 https://conda.anaconda.org/conda-forge/linux-64/xorg-libxt-1.3.0-hd590300_1.conda#ae92aab42726eb29d16488924f7312cb -https://conda.anaconda.org/conda-forge/linux-64/cairo-1.18.0-hbb29018_2.conda#b6d90276c5aee9b4407dd94eb0cd40a8 -https://conda.anaconda.org/conda-forge/linux-64/curl-8.8.0-he654da7_1.conda#78678b2ddfd9bd7c7861b8d2e3b7473b -https://conda.anaconda.org/conda-forge/linux-64/libcblas-3.9.0-22_linux64_openblas.conda#4b31699e0ec5de64d5896e580389c9a1 -https://conda.anaconda.org/conda-forge/linux-64/liblapack-3.9.0-22_linux64_openblas.conda#b083767b6c877e24ee597d93b87ab838 +https://conda.anaconda.org/conda-forge/linux-64/cairo-1.18.0-hebfffa5_3.conda#fceaedf1cdbcb02df9699a0d9b005292 +https://conda.anaconda.org/conda-forge/linux-64/curl-8.9.0-h18eb788_0.conda#cb385c8a955ad49c3342b23cd1a26c11 +https://conda.anaconda.org/conda-forge/linux-64/libcblas-3.9.0-23_linux64_openblas.conda#eede29b40efa878cbe5bdcb767e97310 +https://conda.anaconda.org/conda-forge/linux-64/liblapack-3.9.0-23_linux64_openblas.conda#2af0879961951987e464722fd00ec1e0 https://conda.anaconda.org/conda-forge/linux-64/gsl-2.7-he838d99_0.tar.bz2#fec079ba39c9cca093bf4c00001825de -https://conda.anaconda.org/conda-forge/linux-64/harfbuzz-9.0.0-hfac3d4d_0.conda#c7b47c64af53e8ecee01d101eeab2342 +https://conda.anaconda.org/conda-forge/linux-64/harfbuzz-9.0.0-hda332d3_1.conda#76b32dcf243444aea9c6b804bcfa40b8 https://conda.anaconda.org/conda-forge/linux-64/pango-1.54.0-h4c5309f_1.conda#7df02e445367703cd87a574046e3a6f0 -https://conda.anaconda.org/conda-forge/linux-64/r-base-4.3.3-he2d9a6e_10.conda#f29b857679e49c026984531249e542fd -https://conda.anaconda.org/bioconda/linux-64/nonpareil-3.5.4-r43hdcf5f25_0.tar.bz2#f2ab75cfbe5fa7cc418670ab5becee30 +https://conda.anaconda.org/conda-forge/linux-64/r-base-4.3.3-h9967228_12.conda#88e0b778762c6ffa75241d0f34cfa94e +https://conda.anaconda.org/conda-forge/noarch/r-getopt-1.20.4-r43ha770c72_1.conda#cf6793c369dbc7ef63d9c1bc9b186615 https://conda.anaconda.org/conda-forge/linux-64/r-jsonlite-1.8.8-r43hb1dbf0f_1.conda#eb4377db2a26436aed657474aad972aa +https://conda.anaconda.org/conda-forge/noarch/r-optparse-1.7.5-r43hc72bb7e_1.conda#ae32080aac0f74e73e7cd6e774db1c73 +https://conda.anaconda.org/bioconda/linux-64/nonpareil-3.5.5-r43hdcf5f25_0.tar.bz2#3aa5e80948e3cd9a9dedbf5a201cc66d diff --git a/bio/nonpareil/plot/environment.yaml b/bio/nonpareil/plot/environment.yaml index 848de989bc5..e7aec96bc4f 100644 --- a/bio/nonpareil/plot/environment.yaml +++ b/bio/nonpareil/plot/environment.yaml @@ -3,5 +3,5 @@ channels: - bioconda - nodefaults dependencies: - - nonpareil =3.5.4 + - nonpareil =3.5.5 - r-jsonlite From 60467935840ff3e25cb40c7e16b106ce0fb8b64d Mon Sep 17 00:00:00 2001 From: "snakedeploy-bot[bot]" <115615832+snakedeploy-bot[bot]@users.noreply.github.com> Date: Fri, 26 Jul 2024 05:50:45 +0000 Subject: [PATCH 19/62] perf: autobump bio/taxonkit (#3094) Automatic bump of bio/taxonkit. --------- Co-authored-by: snakedeploy-bot[bot] <115615832+snakedeploy-bot[bot]@users.noreply.github.com> --- bio/taxonkit/environment.linux-64.pin.txt | 2 +- bio/taxonkit/environment.yaml | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/bio/taxonkit/environment.linux-64.pin.txt b/bio/taxonkit/environment.linux-64.pin.txt index 3ba25857252..c91979c031c 100644 --- a/bio/taxonkit/environment.linux-64.pin.txt +++ b/bio/taxonkit/environment.linux-64.pin.txt @@ -2,4 +2,4 @@ # $ conda create --name --file # platform: linux-64 @EXPLICIT -https://conda.anaconda.org/bioconda/linux-64/taxonkit-0.16.0-h9ee0642_0.tar.bz2#d58328deecfbc00948320e07d5a885c4 +https://conda.anaconda.org/bioconda/linux-64/taxonkit-0.17.0-h9ee0642_1.tar.bz2#9dba2510a7b88599a1be245c1d2684e3 diff --git a/bio/taxonkit/environment.yaml b/bio/taxonkit/environment.yaml index a1c16ef2172..967a4876faf 100644 --- a/bio/taxonkit/environment.yaml +++ b/bio/taxonkit/environment.yaml @@ -2,4 +2,4 @@ channels: - bioconda - nodefaults dependencies: - - taxonkit =0.16.0 + - taxonkit =0.17.0 From 1a4ddaade208efed101fb66ba9bb398946f7e807 Mon Sep 17 00:00:00 2001 From: "snakedeploy-bot[bot]" <115615832+snakedeploy-bot[bot]@users.noreply.github.com> Date: Fri, 26 Jul 2024 05:57:53 +0000 Subject: [PATCH 20/62] perf: autobump bio/ucsc/gtfToGenePred (#3095) Automatic bump of bio/ucsc/gtfToGenePred. --------- Co-authored-by: snakedeploy-bot[bot] <115615832+snakedeploy-bot[bot]@users.noreply.github.com> --- .../environment.linux-64.pin.txt | 32 +++++++++---------- bio/ucsc/gtfToGenePred/environment.yaml | 2 +- 2 files changed, 17 insertions(+), 17 deletions(-) diff --git a/bio/ucsc/gtfToGenePred/environment.linux-64.pin.txt b/bio/ucsc/gtfToGenePred/environment.linux-64.pin.txt index c9f5425f6b7..207e796cffc 100644 --- a/bio/ucsc/gtfToGenePred/environment.linux-64.pin.txt +++ b/bio/ucsc/gtfToGenePred/environment.linux-64.pin.txt @@ -3,27 +3,27 @@ # platform: linux-64 @EXPLICIT https://conda.anaconda.org/conda-forge/linux-64/_libgcc_mutex-0.1-conda_forge.tar.bz2#d7c89558ba9fa0495403155b64376d81 -https://conda.anaconda.org/conda-forge/linux-64/ca-certificates-2024.2.2-hbcca054_0.conda#2f4327a1cbe7f022401b236e915a5fef -https://conda.anaconda.org/conda-forge/linux-64/ld_impl_linux-64-2.40-h55db66e_0.conda#10569984e7db886e4f1abc2b47ad79a1 -https://conda.anaconda.org/conda-forge/linux-64/libstdcxx-ng-13.2.0-hc0a3c3a_6.conda#2f18345bbc433c8a1ed887d7161e86a6 +https://conda.anaconda.org/conda-forge/linux-64/ca-certificates-2024.7.4-hbcca054_0.conda#23ab7665c5f63cfb9f1f6195256daac6 +https://conda.anaconda.org/conda-forge/linux-64/ld_impl_linux-64-2.40-hf3520f5_7.conda#b80f2f396ca2c28b8c14c437a4ed1e74 https://conda.anaconda.org/conda-forge/linux-64/python_abi-3.12-4_cp312.conda#dccc2d142812964fcc6abdc97b672dff https://conda.anaconda.org/conda-forge/noarch/tzdata-2024a-h0c530f3_0.conda#161081fc7cec0bfda0d86d7cb595f8d8 -https://conda.anaconda.org/conda-forge/linux-64/libgomp-13.2.0-h77fa898_6.conda#e733e0573651a1f0639fa8ce066a286e +https://conda.anaconda.org/conda-forge/linux-64/libgomp-14.1.0-h77fa898_0.conda#ae061a5ed5f05818acdf9adab72c146d https://conda.anaconda.org/conda-forge/linux-64/_openmp_mutex-4.5-2_gnu.tar.bz2#73aaf86a425cc6e73fcf236a5a46396d -https://conda.anaconda.org/conda-forge/linux-64/libgcc-ng-13.2.0-h77fa898_6.conda#4398809ac84d0b8c28beebaaa83277f5 -https://conda.anaconda.org/conda-forge/linux-64/bzip2-1.0.8-hd590300_5.conda#69b8b6202a07720f448be700e300ccf4 -https://conda.anaconda.org/conda-forge/linux-64/icu-73.2-h59595ed_0.conda#cc47e1facc155f91abd89b11e48e72ff +https://conda.anaconda.org/conda-forge/linux-64/libgcc-ng-14.1.0-h77fa898_0.conda#ca0fad6a41ddaef54a153b78eccb5037 +https://conda.anaconda.org/conda-forge/linux-64/bzip2-1.0.8-h4bc722e_7.conda#62ee74e96c5ebb0af99386de58cf9553 https://conda.anaconda.org/conda-forge/linux-64/libexpat-2.6.2-h59595ed_0.conda#e7ba12deb7020dd080c6c70e7b6f6a3d https://conda.anaconda.org/conda-forge/linux-64/libffi-3.4.2-h7f98852_5.tar.bz2#d645c6d2ac96843a2bfaccd2d62b3ac3 https://conda.anaconda.org/conda-forge/linux-64/libnsl-2.0.1-hd590300_0.conda#30fd6e37fe21f86f4bd26d6ee73eeec7 +https://conda.anaconda.org/conda-forge/linux-64/libstdcxx-ng-14.1.0-hc0a3c3a_0.conda#1cb187a157136398ddbaae90713e2498 https://conda.anaconda.org/conda-forge/linux-64/libuuid-2.38.1-h0b41bf4_0.conda#40b61aab5c7ba9ff276c41cfffe6b80b https://conda.anaconda.org/conda-forge/linux-64/libxcrypt-4.4.36-hd590300_1.conda#5aa797f8787fe7a17d1b0821485b5adc -https://conda.anaconda.org/conda-forge/linux-64/libzlib-1.2.13-hd590300_5.conda#f36c115f1ee199da648e0597ec2047ad -https://conda.anaconda.org/conda-forge/linux-64/ncurses-6.4.20240210-h59595ed_0.conda#97da8860a0da5413c7c98a3b3838a645 -https://conda.anaconda.org/conda-forge/linux-64/openssl-3.3.0-hd590300_0.conda#c0f3abb4a16477208bbd43a39bd56f18 +https://conda.anaconda.org/conda-forge/linux-64/libzlib-1.2.13-h4ab18f5_6.conda#27329162c0dc732bcf67a4e0cd488125 +https://conda.anaconda.org/conda-forge/linux-64/ncurses-6.5-h59595ed_0.conda#fcea371545eda051b6deafb24889fc69 +https://conda.anaconda.org/conda-forge/linux-64/openssl-3.3.1-h4bc722e_2.conda#e1b454497f9f7c1147fdde4b53f1b512 https://conda.anaconda.org/conda-forge/linux-64/xz-5.2.6-h166bdaf_0.tar.bz2#2161070d867d1b1204ea749c8eec4ef0 +https://conda.anaconda.org/conda-forge/linux-64/icu-75.1-he02047a_0.conda#8b189310083baabfb622af68fd9d3ae3 https://conda.anaconda.org/conda-forge/linux-64/libpng-1.6.43-h2797004_0.conda#009981dd9cfcaa4dbfa25ffaed86bcae -https://conda.anaconda.org/conda-forge/linux-64/libsqlite-3.45.3-h2797004_0.conda#b3316cbe90249da4f8e84cd66e1cc55b +https://conda.anaconda.org/conda-forge/linux-64/libsqlite-3.46.0-hde9e2c9_0.conda#18aa975d2094c34aef978060ae7da7d8 https://conda.anaconda.org/conda-forge/linux-64/mysql-connector-c-6.1.11-h659d440_1008.conda#149e0b89cbbe09397f1147cb3736bcbe https://conda.anaconda.org/conda-forge/linux-64/readline-8.2-h8228510_1.conda#47d31b792659ce70f470b5c82fdfb7a4 https://conda.anaconda.org/conda-forge/linux-64/tk-8.6.13-noxft_h4845f30_101.conda#d453b98d9c83e71da0741bb0ff4d76bc @@ -37,7 +37,7 @@ https://conda.anaconda.org/conda-forge/noarch/parsedatetime-2.4-py_1.tar.bz2#8df https://conda.anaconda.org/conda-forge/noarch/pycparser-2.22-pyhd8ed1ab_0.conda#844d9eb3b43095b031874477f7d70088 https://conda.anaconda.org/conda-forge/noarch/pytimeparse-1.1.8-py_0.tar.bz2#edde7e7260599f9860002187486b3e01 https://conda.anaconda.org/conda-forge/noarch/pytz-2024.1-pyhd8ed1ab_0.conda#3eeeeb9e4827ace8c0c1419c85d590ad -https://conda.anaconda.org/conda-forge/noarch/setuptools-69.5.1-pyhd8ed1ab_0.conda#7462280d81f639363e6e63c81276bd9e +https://conda.anaconda.org/conda-forge/noarch/setuptools-71.0.4-pyhd8ed1ab_0.conda#ee78ac9c720d0d02fcfd420866b82ab1 https://conda.anaconda.org/conda-forge/noarch/six-1.16.0-pyh6c4a22f_0.tar.bz2#e5f25f8dbc060e9a8d912e432202afc2 https://conda.anaconda.org/conda-forge/noarch/text-unidecode-1.3-pyhd8ed1ab_1.conda#ba8aba332d8868897ce44ad74015a7fe https://conda.anaconda.org/conda-forge/noarch/wheel-0.43.0-pyhd8ed1ab_1.conda#0b5293a157c2b5cd513dd1b03d8d3aae @@ -46,14 +46,14 @@ https://conda.anaconda.org/conda-forge/noarch/babel-2.14.0-pyhd8ed1ab_0.conda#96 https://conda.anaconda.org/conda-forge/linux-64/cffi-1.16.0-py312hf06ca03_0.conda#56b0ca764ce23cc54f3f7e2a7b970f6d https://conda.anaconda.org/conda-forge/noarch/isodate-0.6.1-pyhd8ed1ab_0.tar.bz2#4a62c93c1b5c0b920508ae3fd285eaf5 https://conda.anaconda.org/conda-forge/noarch/leather-0.3.4-pyhd8ed1ab_0.tar.bz2#513f26ec3c158a325b16df2da418df82 -https://conda.anaconda.org/conda-forge/linux-64/openpyxl-3.1.2-py312h98912ed_1.conda#7f4e257ea4714e9166a93b733b26c2da +https://conda.anaconda.org/conda-forge/linux-64/openpyxl-3.1.4-py312h98912ed_0.conda#678227a6922230b10dbf93b8d161c38d https://conda.anaconda.org/conda-forge/noarch/pip-24.0-pyhd8ed1ab_0.conda#f586ac1e56c8638b64f9c8122a7b8a67 https://conda.anaconda.org/conda-forge/noarch/python-slugify-8.0.4-pyhd8ed1ab_0.conda#4b11845622b3c3178c0e989235b53975 https://conda.anaconda.org/conda-forge/linux-64/sqlalchemy-1.4.49-py312h98912ed_1.conda#755a7fbdcbf783fe197b2367ed944f86 https://conda.anaconda.org/conda-forge/linux-64/cld2-cffi-0.1.4-py312h30efb56_1005.conda#3a8ba4ad9ab365e3cbe610819f206603 -https://conda.anaconda.org/conda-forge/linux-64/pyicu-2.13.1-py312h62d7e36_0.conda#55efd4e4e21b898b87ee2c65b9ed9504 -https://conda.anaconda.org/conda-forge/noarch/agate-1.10.2-pyh707e725_0.conda#7edca1d1735bf01f9a2bb4372a9436fb +https://conda.anaconda.org/conda-forge/linux-64/pyicu-2.13.1-py312h5c10c66_1.conda#d0ba0a8a2fe1324ce74475b5a32e3cd8 +https://conda.anaconda.org/conda-forge/noarch/agate-1.11.0-pyh707e725_0.conda#65a4cc6ffe639ccecb6a4341950d240e https://conda.anaconda.org/conda-forge/noarch/agate-dbf-0.2.3-pyhd8ed1ab_0.conda#9e33e31e72d8bbe2d96b49c9a534ba2f https://conda.anaconda.org/conda-forge/noarch/agate-excel-0.2.3-py_0.tar.bz2#26a3416153f17addfdab82a183665a98 https://conda.anaconda.org/conda-forge/noarch/agate-sql-0.7.2-pyhd8ed1ab_0.conda#6279859d84efb3bf26ccd89b47278711 -https://conda.anaconda.org/conda-forge/noarch/csvkit-2.0.0-pyhd8ed1ab_0.conda#eb7d286b58d94901501c31b926f44df6 +https://conda.anaconda.org/conda-forge/noarch/csvkit-2.0.1-pyhd8ed1ab_0.conda#51f040267b6d3e749c60fbbc032d5bd2 diff --git a/bio/ucsc/gtfToGenePred/environment.yaml b/bio/ucsc/gtfToGenePred/environment.yaml index 9bcc2921bea..3e3a698026b 100644 --- a/bio/ucsc/gtfToGenePred/environment.yaml +++ b/bio/ucsc/gtfToGenePred/environment.yaml @@ -4,4 +4,4 @@ channels: - nodefaults dependencies: - ucsc-gtftogenepred =447 - - csvkit =2.0.0 + - csvkit =2.0.1 From a192628ce9523c0c0523e619571c3ca050187dca Mon Sep 17 00:00:00 2001 From: "snakedeploy-bot[bot]" <115615832+snakedeploy-bot[bot]@users.noreply.github.com> Date: Fri, 26 Jul 2024 06:00:10 +0000 Subject: [PATCH 21/62] perf: autobump bio/unicycler (#2987) Automatic bump of bio/unicycler. --------- Co-authored-by: snakedeploy-bot[bot] <115615832+snakedeploy-bot[bot]@users.noreply.github.com> --- bio/unicycler/environment.linux-64.pin.txt | 121 +++++++++++---------- bio/unicycler/environment.yaml | 4 +- 2 files changed, 63 insertions(+), 62 deletions(-) diff --git a/bio/unicycler/environment.linux-64.pin.txt b/bio/unicycler/environment.linux-64.pin.txt index b130fb74a39..1edc555c4e0 100644 --- a/bio/unicycler/environment.linux-64.pin.txt +++ b/bio/unicycler/environment.linux-64.pin.txt @@ -3,53 +3,45 @@ # platform: linux-64 @EXPLICIT https://conda.anaconda.org/conda-forge/linux-64/_libgcc_mutex-0.1-conda_forge.tar.bz2#d7c89558ba9fa0495403155b64376d81 -https://conda.anaconda.org/conda-forge/noarch/_sysroot_linux-64_curr_repodata_hack-3-h69a702a_14.conda#38d211c448a67f12fe693fe25df4da23 -https://conda.anaconda.org/conda-forge/linux-64/ca-certificates-2024.2.2-hbcca054_0.conda#2f4327a1cbe7f022401b236e915a5fef +https://conda.anaconda.org/conda-forge/noarch/_sysroot_linux-64_curr_repodata_hack-3-h69a702a_16.conda#1c005af0c6ff22814b7c52ee448d4bea +https://conda.anaconda.org/conda-forge/linux-64/ca-certificates-2024.7.4-hbcca054_0.conda#23ab7665c5f63cfb9f1f6195256daac6 https://conda.anaconda.org/conda-forge/noarch/font-ttf-dejavu-sans-mono-2.37-hab24e00_0.tar.bz2#0c96522c6bdaed4b1566d11387caaf45 https://conda.anaconda.org/conda-forge/noarch/font-ttf-inconsolata-3.000-h77eed37_0.tar.bz2#34893075a5c9e55cdafac56607368fc6 https://conda.anaconda.org/conda-forge/noarch/font-ttf-source-code-pro-2.038-h77eed37_0.tar.bz2#4d59c254e01d9cde7957100457e2d5fb https://conda.anaconda.org/conda-forge/noarch/font-ttf-ubuntu-0.83-h77eed37_2.conda#cbbe59391138ea5ad3658c76912e147f -https://conda.anaconda.org/conda-forge/linux-64/ld_impl_linux-64-2.40-h55db66e_0.conda#10569984e7db886e4f1abc2b47ad79a1 -https://conda.anaconda.org/conda-forge/linux-64/libstdcxx-ng-13.2.0-hc0a3c3a_7.conda#53ebd4c833fa01cb2c6353e99f905406 -https://conda.anaconda.org/conda-forge/linux-64/python_abi-3.10-4_cp310.conda#26322ec5d7712c3ded99dd656142b8ce +https://conda.anaconda.org/conda-forge/linux-64/ld_impl_linux-64-2.40-hf3520f5_7.conda#b80f2f396ca2c28b8c14c437a4ed1e74 +https://conda.anaconda.org/conda-forge/linux-64/python_abi-3.12-4_cp312.conda#dccc2d142812964fcc6abdc97b672dff https://conda.anaconda.org/conda-forge/noarch/tzdata-2024a-h0c530f3_0.conda#161081fc7cec0bfda0d86d7cb595f8d8 https://conda.anaconda.org/conda-forge/noarch/fonts-conda-forge-1-0.tar.bz2#f766549260d6815b0c52253f1fb1bb29 -https://conda.anaconda.org/conda-forge/noarch/kernel-headers_linux-64-3.10.0-h4a8ded7_14.conda#f6c14886b1695a2462d296176e831080 -https://conda.anaconda.org/conda-forge/linux-64/libgomp-13.2.0-h77fa898_7.conda#abf3fec87c2563697defa759dec3d639 +https://conda.anaconda.org/conda-forge/noarch/kernel-headers_linux-64-3.10.0-h4a8ded7_16.conda#ff7f38675b226cfb855aebfc32a13e31 +https://conda.anaconda.org/conda-forge/linux-64/libgomp-14.1.0-h77fa898_0.conda#ae061a5ed5f05818acdf9adab72c146d https://conda.anaconda.org/conda-forge/linux-64/_openmp_mutex-4.5-2_gnu.tar.bz2#73aaf86a425cc6e73fcf236a5a46396d https://conda.anaconda.org/conda-forge/noarch/fonts-conda-ecosystem-1-0.tar.bz2#fee5683a3f04bd15cbd8318b096a27ab -https://conda.anaconda.org/conda-forge/noarch/sysroot_linux-64-2.17-h4a8ded7_14.conda#d5f7a1cca06f56e6ac2b525f199f9b9e -https://conda.anaconda.org/conda-forge/linux-64/libgcc-ng-13.2.0-h77fa898_7.conda#72ec1b1b04c4d15d4204ece1ecea5978 -https://conda.anaconda.org/conda-forge/linux-64/alsa-lib-1.2.11-hd590300_1.conda#0bb492cca54017ea314b809b1ee3a176 -https://conda.anaconda.org/conda-forge/linux-64/bzip2-1.0.8-hd590300_5.conda#69b8b6202a07720f448be700e300ccf4 -https://conda.anaconda.org/conda-forge/linux-64/c-ares-1.28.1-hd590300_0.conda#dcde58ff9a1f30b0037a2315d1846d1f +https://conda.anaconda.org/conda-forge/noarch/sysroot_linux-64-2.17-h4a8ded7_16.conda#223fe8a3ff6d5e78484a9d58eb34d055 +https://conda.anaconda.org/conda-forge/linux-64/libgcc-ng-14.1.0-h77fa898_0.conda#ca0fad6a41ddaef54a153b78eccb5037 +https://conda.anaconda.org/conda-forge/linux-64/alsa-lib-1.2.12-h4ab18f5_0.conda#7ed427f0871fd41cb1d9c17727c17589 +https://conda.anaconda.org/conda-forge/linux-64/bzip2-1.0.8-h4bc722e_7.conda#62ee74e96c5ebb0af99386de58cf9553 +https://conda.anaconda.org/conda-forge/linux-64/c-ares-1.32.3-h4bc722e_0.conda#7624e34ee6baebfc80d67bac76cc9d9d https://conda.anaconda.org/conda-forge/linux-64/gettext-tools-0.22.5-h59595ed_2.conda#985f2f453fb72408d6b6f1be0f324033 https://conda.anaconda.org/conda-forge/linux-64/giflib-5.2.2-hd590300_0.conda#3bf7b9fd5a7136126e0234db4b87c8b6 -https://conda.anaconda.org/conda-forge/linux-64/graphite2-1.3.13-h59595ed_1003.conda#f87c7b7c2cb45f323ffbce941c78ab7c -https://conda.anaconda.org/conda-forge/linux-64/icu-73.2-h59595ed_0.conda#cc47e1facc155f91abd89b11e48e72ff https://conda.anaconda.org/conda-forge/linux-64/keyutils-1.6.1-h166bdaf_0.tar.bz2#30186d27e2c9fa62b45fb1476b7200e3 -https://conda.anaconda.org/conda-forge/linux-64/lerc-4.0.0-h27087fc_0.tar.bz2#76bbff344f0134279f225174e9064c8f -https://conda.anaconda.org/conda-forge/linux-64/libasprintf-0.22.5-h661eb56_2.conda#dd197c968bf9760bba0031888d431ede https://conda.anaconda.org/conda-forge/linux-64/libdeflate-1.20-hd590300_0.conda#8e88f9389f1165d7c0936fe40d9a9a79 https://conda.anaconda.org/conda-forge/linux-64/libev-4.33-hd590300_2.conda#172bf1cd1ff8629f2b1179945ed45055 https://conda.anaconda.org/conda-forge/linux-64/libexpat-2.6.2-h59595ed_0.conda#e7ba12deb7020dd080c6c70e7b6f6a3d https://conda.anaconda.org/conda-forge/linux-64/libffi-3.4.2-h7f98852_5.tar.bz2#d645c6d2ac96843a2bfaccd2d62b3ac3 https://conda.anaconda.org/conda-forge/linux-64/libgettextpo-0.22.5-h59595ed_2.conda#172bcc51059416e7ce99e7b528cede83 -https://conda.anaconda.org/conda-forge/linux-64/libgfortran5-13.2.0-hca663fb_7.conda#c0bd771f09a326fdcd95a60b617795bf +https://conda.anaconda.org/conda-forge/linux-64/libgfortran5-14.1.0-hc5f4f2c_0.conda#6456c2620c990cd8dde2428a27ba0bc5 https://conda.anaconda.org/conda-forge/linux-64/libiconv-1.17-hd590300_2.conda#d66573916ffcf376178462f1b61c941e https://conda.anaconda.org/conda-forge/linux-64/libjpeg-turbo-3.0.0-hd590300_1.conda#ea25936bb4080d843790b586850f82b8 https://conda.anaconda.org/conda-forge/linux-64/libnsl-2.0.1-hd590300_0.conda#30fd6e37fe21f86f4bd26d6ee73eeec7 +https://conda.anaconda.org/conda-forge/linux-64/libstdcxx-ng-14.1.0-hc0a3c3a_0.conda#1cb187a157136398ddbaae90713e2498 https://conda.anaconda.org/conda-forge/linux-64/libunistring-0.9.10-h7f98852_0.tar.bz2#7245a044b4a1980ed83196176b78b73a https://conda.anaconda.org/conda-forge/linux-64/libuuid-2.38.1-h0b41bf4_0.conda#40b61aab5c7ba9ff276c41cfffe6b80b https://conda.anaconda.org/conda-forge/linux-64/libwebp-base-1.4.0-hd590300_0.conda#b26e8aa824079e1be0294e7152ca4559 https://conda.anaconda.org/conda-forge/linux-64/libxcrypt-4.4.36-hd590300_1.conda#5aa797f8787fe7a17d1b0821485b5adc -https://conda.anaconda.org/conda-forge/linux-64/libzlib-1.2.13-hd590300_5.conda#f36c115f1ee199da648e0597ec2047ad -https://conda.anaconda.org/conda-forge/linux-64/llvm-openmp-8.0.1-hc9558a2_0.tar.bz2#67590caab043d6d7ffc371f9cced7848 -https://conda.anaconda.org/bioconda/linux-64/ncbi-vdb-3.1.1-h4ac6f70_0.tar.bz2#4cbc542ee7db0710bdf07a4e55f5daaf +https://conda.anaconda.org/conda-forge/linux-64/libzlib-1.3.1-h4ab18f5_1.conda#57d7dc60e9325e3de37ff8dffd18e814 https://conda.anaconda.org/conda-forge/linux-64/ncurses-6.5-h59595ed_0.conda#fcea371545eda051b6deafb24889fc69 -https://conda.anaconda.org/conda-forge/linux-64/openssl-3.3.0-h4ab18f5_3.conda#12ea6d0d4ed54530eaed18e4835c1f7c -https://conda.anaconda.org/conda-forge/linux-64/pcre-8.45-h9c3ff4c_0.tar.bz2#c05d1820a6d34ff07aaaab7a9b7eddaa -https://conda.anaconda.org/conda-forge/linux-64/pixman-0.43.2-h59595ed_0.conda#71004cbf7924e19c02746ccde9fd7123 +https://conda.anaconda.org/conda-forge/linux-64/openssl-3.3.1-h4bc722e_2.conda#e1b454497f9f7c1147fdde4b53f1b512 https://conda.anaconda.org/conda-forge/linux-64/pthread-stubs-0.4-h36c2ea0_1001.tar.bz2#22dad4df6e8630e8dff2428f6f6a7036 https://conda.anaconda.org/conda-forge/linux-64/xorg-inputproto-2.3.2-h7f98852_1002.tar.bz2#bcd1b3396ec6960cbc1d2855a9e60b2b https://conda.anaconda.org/conda-forge/linux-64/xorg-kbproto-1.0.7-h7f98852_1002.tar.bz2#4b230e8381279d76131116660f5a241a @@ -62,33 +54,40 @@ https://conda.anaconda.org/conda-forge/linux-64/xorg-xextproto-7.3.0-h0b41bf4_10 https://conda.anaconda.org/conda-forge/linux-64/xorg-xproto-7.0.31-h7f98852_1007.tar.bz2#b4a4381d54784606820704f7b5f05a15 https://conda.anaconda.org/conda-forge/linux-64/xz-5.2.6-h166bdaf_0.tar.bz2#2161070d867d1b1204ea749c8eec4ef0 https://conda.anaconda.org/conda-forge/linux-64/expat-2.6.2-h59595ed_0.conda#53fb86322bdb89496d7579fe3f02fd61 -https://conda.anaconda.org/conda-forge/linux-64/libasprintf-devel-0.22.5-h661eb56_2.conda#02e41ab5834dcdcc8590cf29d9526f50 +https://conda.anaconda.org/conda-forge/linux-64/graphite2-1.3.13-h59595ed_1003.conda#f87c7b7c2cb45f323ffbce941c78ab7c +https://conda.anaconda.org/conda-forge/linux-64/icu-75.1-he02047a_0.conda#8b189310083baabfb622af68fd9d3ae3 +https://conda.anaconda.org/conda-forge/linux-64/lerc-4.0.0-h27087fc_0.tar.bz2#76bbff344f0134279f225174e9064c8f +https://conda.anaconda.org/conda-forge/linux-64/libasprintf-0.22.5-h661eb56_2.conda#dd197c968bf9760bba0031888d431ede 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@@ dependencies: - samtools =1.20 - pilon =1.24 - racon =1.5.0 - - blast =2.15.0 - - unicycler =0.5.0 + - blast =2.16.0 + - unicycler =0.5.1 From 14f8ab8bcde3e80c7afec8fa4c80d93b1ec2f44e Mon Sep 17 00:00:00 2001 From: David Laehnemann Date: Wed, 31 Jul 2024 22:15:52 +0200 Subject: [PATCH 22/62] docs: major overhaul of contribution guidelines and documentation (#3076) This pull request is a major overhaul of the contribution guidelines. It updates it to the current best practices and also cleans up the `I confirm that:` list in the pull request template. Hopefully, this makes contributing (and improving) wrappers a little bit easier. ### QC * [x] I confirm that: For all wrappers added by this PR, * there is a test case which covers any introduced changes, * `input:` and `output:` file paths in the resulting rule can be changed arbitrarily, * either the wrapper can only use a single core, or the example rule contains a `threads: x` statement with `x` being a reasonable default, * rule names in the test case are in [snake_case](https://en.wikipedia.org/wiki/Snake_case) and somehow tell what the rule is about or match the tools purpose or name (e.g., `map_reads` for a step that maps reads), * all `environment.yaml` specifications follow [the respective best practices](https://stackoverflow.com/a/64594513/2352071), * the `environment.yaml` pinning has been updated by running `snakedeploy pin-conda-envs environment.yaml` on a linux machine, * wherever possible, command line arguments are inferred and set automatically (e.g. based on file extensions in `input:` or `output:`), * all fields of the example rules in the `Snakefile`s and their entries are explained via comments (`input:`/`output:`/`params:` etc.), * `stderr` and/or `stdout` are logged correctly (`log:`), depending on the wrapped tool, * temporary files are either written to a unique hidden folder in the working directory, or (better) stored where the Python function `tempfile.gettempdir()` points to (see [here](https://docs.python.org/3/library/tempfile.html#tempfile.gettempdir); this also means that using any Python `tempfile` default behavior works), * the `meta.yaml` contains a link to the documentation of the respective tool or command, * `Snakefile`s pass the linting (`snakemake --lint`), * `Snakefile`s are formatted with [snakefmt](https://github.com/snakemake/snakefmt), * Python wrapper scripts are formatted with [black](https://black.readthedocs.io). * Conda environments use a minimal amount of channels, in recommended ordering. E.g. for bioconda, use (conda-forge, bioconda, nodefaults, as conda-forge should have highest priority and defaults channels are usually not needed because most packages are in conda-forge nowadays). --------- Co-authored-by: Filipe G. Vieira <1151762+fgvieira@users.noreply.github.com> --- .github/pull_request_template.md | 26 ++-- docs/contributing.rst | 211 +++++++++++++++++++++++++------ 2 files changed, 182 insertions(+), 55 deletions(-) diff --git a/.github/pull_request_template.md b/.github/pull_request_template.md index 2d3457e81c2..159e7f1e2ca 100644 --- a/.github/pull_request_template.md +++ b/.github/pull_request_template.md @@ -6,22 +6,12 @@ ### QC -* [ ] I confirm that: +* [ ] I confirm that I have followed the [documentation for contributing to `snakemake-wrappers`](https://snakemake-wrappers.readthedocs.io/en/stable/contributing.html). -For all wrappers added by this PR, - -* there is a test case which covers any introduced changes, -* `input:` and `output:` file paths in the resulting rule can be changed arbitrarily, -* either the wrapper can only use a single core, or the example rule contains a `threads: x` statement with `x` being a reasonable default, -* rule names in the test case are in [snake_case](https://en.wikipedia.org/wiki/Snake_case) and somehow tell what the rule is about or match the tools purpose or name (e.g., `map_reads` for a step that maps reads), -* all `environment.yaml` specifications follow [the respective best practices](https://stackoverflow.com/a/64594513/2352071), -* the `environment.yaml` pinning has been updated by running `snakedeploy pin-conda-envs environment.yaml` on a linux machine, -* wherever possible, command line arguments are inferred and set automatically (e.g. based on file extensions in `input:` or `output:`), -* all fields of the example rules in the `Snakefile`s and their entries are explained via comments (`input:`/`output:`/`params:` etc.), -* `stderr` and/or `stdout` are logged correctly (`log:`), depending on the wrapped tool, -* temporary files are either written to a unique hidden folder in the working directory, or (better) stored where the Python function `tempfile.gettempdir()` points to (see [here](https://docs.python.org/3/library/tempfile.html#tempfile.gettempdir); this also means that using any Python `tempfile` default behavior works), -* the `meta.yaml` contains a link to the documentation of the respective tool or command, -* `Snakefile`s pass the linting (`snakemake --lint`), -* `Snakefile`s are formatted with [snakefmt](https://github.com/snakemake/snakefmt), -* Python wrapper scripts are formatted with [black](https://black.readthedocs.io). -* Conda environments use a minimal amount of channels, in recommended ordering. E.g. for bioconda, use (conda-forge, bioconda, nodefaults, as conda-forge should have highest priority and defaults channels are usually not needed because most packages are in conda-forge nowadays). +While the contributions guidelines are more extensive, please particularly ensure that: +* [ ] `test.py` was updated to call any added or updated example rules in a `Snakefile` +* [ ] `input:` and `output:` file paths in the rules can be chosen arbitrarily +* [ ] wherever possible, command line arguments are inferred and set automatically (e.g. based on file extensions in `input:` or `output:`) +* [ ] temporary files are either written to a unique hidden folder in the working directory, or (better) stored where the Python function `tempfile.gettempdir()` points to +* [ ] the `meta.yaml` contains a link to the documentation of the respective tool or command under `url:` +* [ ] conda environments use a minimal amount of channels and packages, in recommended ordering diff --git a/docs/contributing.rst b/docs/contributing.rst index 4d30670c74a..64800c7aea3 100644 --- a/docs/contributing.rst +++ b/docs/contributing.rst @@ -14,31 +14,60 @@ If you want to contribute we suggest the following procedure: The pull request will be reviewed and included as fast as possible. If your pull request does not get a review quickly, you can `@mention ` previous contributors to a particular wrapper (``git blame``) or regular contributors that you think might be able to give a review. -Contributions should follow the coding style of the already present examples, i.e.: - -* provide a ``meta.yaml`` that describes the wrapper (see the `meta.yaml documentation below `_) -* provide an ``environment.yaml`` which lists all required software packages and follows - `the respective best practices `_. The - packages should be available for installation via the - `default anaconda channels `_ or via the - `conda`_ channels - `bioconda `_ or - `conda-forge `_. - Other sustainable community maintained channels are possible as well. -* add a ``wrapper.py`` or ``wrapper.R`` file that can deal with arbitrary ``input:`` and ``output:`` paths. -* provide a minimal test case in a subfolder called ``test``, with an example - ``Snakefile`` that shows how to use the wrapper (rule names should be descriptive and written in `snake_case `_), some minimal testing data - (also check existing wrappers for suitable data) and add an invocation of the - test in ``test.py`` -* ensure consistent `formatting`_ of Python files and `linting`_ of Snakefiles. + +In general, always take inspiration from existing wrappers. +And then, contributions should: + +* provide the following files: + + * ``meta.yaml`` (wrapper description), see :ref:`meta` + * ``environment.yaml`` (required software), see :ref:`environment` + * ``environment.linux-64.pin.yaml`` (autogenerated pinning of the software), see :ref:`environment` + * ``wrapper.py`` or ``wrapper.R`` (actual wrapper code), see :ref:`wrapper` + * ``test/Snakefile`` (minimal test cases and copy-pasteable examples), see :ref:`Snakefile` + +* amend ``test.py`` to call all of the testing rules provided in ``test/Snakefile``, see :ref:`test` +* ensure consistent: + + * `formatting`_ of Python files + * `linting`_ of Snakefiles + + +.. _development environment: + +``conda``/``mamba`` environment for development +----------------------------------------------- + +To have all the tools you need for developing and testing wrappers in one single ``conda``/``mamba`` environment: + +1. `Install miniforge `_. +2. Set up the channels as `described for bioconda `_. +3. Create an environment with the necessary dependencies: + +.. code-block:: bash + + mamba create -n snakemake-wrappers-development -c conda-forge -c bioconda snakemake snakefmt snakedeploy black mamba pytest + +4. Activate the environment with: + +.. code-block:: bash + + mamba activate snakemake-wrappers-development + .. _meta: ``meta.yaml`` file ------------------- -The following fields are available to use in the wrapper ``meta.yaml`` file. All, except -those marked optional, should be provided. +This file describes the wrapper and how to use it. + +The general file syntax is `YAML`_. +Text / strings (values in a `YAML`_ `mapping`_ or `sequence`_), can use `reStructuredText`_ syntax. + +The following fields are available to use in the wrapper ``meta.yaml`` file. +All, except those marked optional, should be provided. +Especially make sure to include a URL of the respective tool's documentation. * **name**: The name of the wrapper. * **description**: a description of what the wrapper does. @@ -49,7 +78,8 @@ those marked optional, should be provided. * **params** (optional): A `mapping`_ of parameters that can be used in the wrapper's ``params`` directive. If no parameters are used for the wrapper, this field can be omitted. * **notes** (optional): Anything of note that does not fit into the scope of the other fields. -You can add a newline to the rendered text in these fields with the addition of ``|nl|`` +You can add a newline to the rendered text in these fields with the addition of ``|nl|``. + Example ^^^^^^^ @@ -77,9 +107,117 @@ Example notes: Multiple threads can be used during compression of the output file with ``pigz``. +.. _YAML: https://yaml.org/spec/1.2.2/ +.. _sequence: https://yaml.org/spec/1.2.2/#21-collections +.. _mapping: https://yaml.org/spec/1.2.2/#21-collections +.. _reStructuredText: https://www.sphinx-doc.org/en/master/usage/restructuredtext/basics.html + + +.. _environment: + +``environment.yaml`` file +------------------------- + +This file needs to list all the software that the wrapper code needes to run successfully. + +For all software following `semantic versioning `_ conventions, specify (and thus pin) the major and minor version, but leave the patch version unspecified. +Also, unless this is needed to work around version incompatibilities not properly handled by the conda packages themselves, only specify the actual software needed and let ``conda``/``mamba`` determine the dependencies. + +To make sure that ``conda``/``mamba`` knows where to look for the package, include a list of all of the conda channels that the software and its dependencies require. +This will usually include `conda-forge `_, as it contains many essential libraries that other packages and tools depend on. +This channel should usually be specified first, to make sure it takes precedence (``snakemake`` asks users to ``conda config --set channel_priority strict``). +In addition, you may need to include other sustainable community maintained channels (like `bioconda `_). +And as the last channel specification, always include ``nodefaults``. +This avoids software dependency conflicts between the ``conda-forge`` channel and the ``default`` channels that should not be needed nowadays. + +Finally, make sure to run ``snakedeploy pin-conda-envs environment.yaml`` on the finished environment specification. +This will generate a file called ``environment.linux-64.pin.txt`` with all the dependency versions determined by ``conda``/``mamba``, ensuring that a particular wrapper version will always generate the exact same environment with the exact package versions from this file. +You should include this pinning file in the pull request for your wrapper. + +Example +^^^^^^^ + +.. code-block:: yaml + + channels: + - conda-forge + - bioconda + - nodefaults + dependencies: + - bioconductor-biomart =2.58 + - r-nanoparquet =0.3 + - r-tidyverse = 2.0 + + +.. _wrapper: + +``wrapper.py`` or ``wrapper.R`` file +------------------------------------ + +This is the actual code that the wrapper executes. +It is handled like an `external script in snakemake `_, so you have the respective `snakemake` objects available. + +Please ensure that the wrapper: + +* can deal with arbitrary ``input:`` and ``output:`` paths and filenames +* redirects `stdout` and `stderr` to log files specified by the `log:` directive (typical boilerplate code can for example be found in `this knowledge base `_) +* automatically infers command line arguments wherever possible (for example based on file extensions in ``input:`` and ``output:``) +* passes on the `threads` value, if the used tool(s) allow(s) it +* writes any temporary files to a unique hidden folder in the working directory, or (better) stores them where the Python function `tempfile.gettempdir() `_ points (this also means that using any Python tempfile default behavior works) +* is formatted according to the language's standards (for Python, format it with `black `_: ``black wrapper.py``) + +For repeatedly needed functionality you can use the `snakemake-wrapper-utils `_. +Use what is available or create new functionality there, whenever you start repeating functions across wrappers. +Examples of this are: + +1. The command line argument parsing for a software tool like ``samtools`` where you create one wrapper each for a number of different subcommands that share the main arguments. See the `samtools.py `_ utility functions for the respective functionality. +2. The handling of recurring Java options, for example things like memory handling. See `java.py `_ for the respective functionality. + +To use ``snakemake-wrapper-utils``, you have to include them as a depenency in your :ref:`environment` definition file and import the respective function(s) in your :ref:`wrapper` script (for example ``from snakemake_wrapper_utils.java import get_java_opts``). + + +.. _snakefile: + +``test/Snakefile`` file +----------------------- + +In a subfolder called ``test``, create a ``Snakefile`` with example invocations of the wrapper. +These examples should comprehensively showcase the available functionality of the wrapper, as they serve as both the copy-pasteable examples rendered in the documentation, and the test cases run in the continuous integration testing (make sure to include calls to the rules in ``test.py``, see :ref:`test`). +If these rules need any input data, you can also include minimal (small) testing data in the ``test/`` folder (also check existing wrappers for suitable data). + +When writing the ``Snakefile``, please ensure that: + +* rule names in the examples are in `snake_case `_ and descriptive (they should explain what the rule is does, or match the tool's purpose or name; for example ``map_reads`` for a step that maps reads) +* it is formatted correctly by running `snakefmt `_ (``snakefmt Snakefile``) +* it also passes linting, see :ref:`linting` +* all example rules in your ``test/Snakefile`` have an invocation as a test case in ``test.py``, see :ref:`test` +* wherever you can do this with a short comment, explain possible settings for all keywords like ``input:``, ``output:``, ``params:``, ``threads:``, etc. (provide longer explanations in the :ref:`meta` file) +* provide a sensible default for ``threads:``, if more than one thread can be used by the wrapper + +.. _test: + +``test.py`` tests file +---------------------- + +Every example rule listed in a :ref:`snakefile`, should be included as a test case in ``test.py``. +The easiest way is usually to duplicate an existing test and adapt it to your newly added example rule. + +When done editing, make sure that ``test.py`` :ref:`formatting` still follows |black|_ standards. + +Example +^^^^^^^ + +.. code-block:: python + + @skip_if_not_modified + def test_bcftools_sort(): + run( + "bio/bcftools/sort", + ["snakemake", "--cores", "1", "--use-conda", "-F", "a.sorted.bcf"], + ) + + -.. _sequence: https://yaml.org/spec/1.2/spec.html#id2759963 -.. _mapping: https://yaml.org/spec/1.2/spec.html#id2759963 .. _formatting: @@ -108,35 +246,34 @@ Please `lint`_ your test ``Snakefile`` with:: Testing locally --------------- -If you want to debug your contribution locally (before creating a pull request), you -can install all dependencies with |mamba|_ (or |conda|_). `Install miniconda with the -channels as described for bioconda `_ and -set up an environment with the necessary dependencies and activate it:: - - mamba create -n test-snakemake-wrappers snakemake pytest conda snakefmt black - conda activate test-snakemake-wrappers +If you want to debug your contribution locally before creating a pull request, ensure you have the :ref:`development environment` installed and activated. Afterwards, from the main directory of the repo, you can run the test(s) for your contribution by `specifying an expression `_ -that matches the name(s) of your test(s) via the ``-k`` option of ``pytest``:: +that matches the name(s) of your test(s) via the ``-k`` option of ``pytest``: + +.. code-block:: bash pytest test.py -v -k your_test If you also want to test the docs generation locally, create another environment -and activate it:: +and activate it: + +.. code-block:: bash + + mamba create -n test-snakemake-wrapper-docs -c conda-forge sphinx sphinx_rtd_theme pyyaml sphinx-copybutton sphinxawesome_theme myst-parser + mamba activate test-snakemake-wrapper-docs - mamba create -n test-snakemake-wrapper-docs sphinx sphinx_rtd_theme pyyaml sphinx-copybutton - conda activate test-snakemake-wrapper-docs +Then, enter the respective directory and build the docs: -Then, enter the respective directory and build the docs:: +.. code-block:: bash cd docs make html -If it runs through, you can open the main page at ``docs/_build/html/index.html`` -in a web browser. If you want to start fresh, you can clean up the build -with ``make clean``. +If it runs through, you can open the main page at ``docs/_build/html/index.html`` in a web browser. +If you want to start fresh, you can clean up the build with ``make clean``. .. |mamba| replace:: ``mamba`` From a6234bbedbb451050718bc9fe0a8a3619976d7b0 Mon Sep 17 00:00:00 2001 From: "github-actions[bot]" <41898282+github-actions[bot]@users.noreply.github.com> Date: Wed, 31 Jul 2024 22:31:01 +0200 Subject: [PATCH 23/62] chore: release 3.14.0 (#3077) :robot: I have created a release \*beep\* \*boop\* --- ## [3.14.0](https://www.github.com/snakemake/snakemake-wrappers/compare/v3.13.8...v3.14.0) (2024-07-31) ### Features * add new wrapper to create annotation tables via Ensembl biomart ([#3072](https://www.github.com/snakemake/snakemake-wrappers/issues/3072)) ([07dc088](https://www.github.com/snakemake/snakemake-wrappers/commit/07dc08890bea0c13056d70f17a247f46c99e00ab)) ### Performance Improvements * autobump bio/blast/blastn ([#3080](https://www.github.com/snakemake/snakemake-wrappers/issues/3080)) ([bc0b80d](https://www.github.com/snakemake/snakemake-wrappers/commit/bc0b80db175c25a04cc2c4a3cd665f6be297741b)) * autobump bio/blast/makeblastdb ([#3078](https://www.github.com/snakemake/snakemake-wrappers/issues/3078)) ([86ec876](https://www.github.com/snakemake/snakemake-wrappers/commit/86ec8769ddb9a881ca28d0b4600e24b5f9d41229)) * autobump bio/bwa/mem ([#3079](https://www.github.com/snakemake/snakemake-wrappers/issues/3079)) ([01dc16f](https://www.github.com/snakemake/snakemake-wrappers/commit/01dc16fdebfab3ee6f36983a317fc8ea731f1d44)) * autobump bio/entrez/efetch ([#3081](https://www.github.com/snakemake/snakemake-wrappers/issues/3081)) ([f178d5f](https://www.github.com/snakemake/snakemake-wrappers/commit/f178d5f1da9a8f420a1e1f8f08053f3983dc11e0)) * autobump bio/fgbio/annotatebamwithumis ([#3082](https://www.github.com/snakemake/snakemake-wrappers/issues/3082)) ([b902adf](https://www.github.com/snakemake/snakemake-wrappers/commit/b902adfb65d0ea18dc557b25aa98031a394a99c8)) * autobump bio/fgbio/callmolecularconsensusreads ([#3085](https://www.github.com/snakemake/snakemake-wrappers/issues/3085)) ([5727f2d](https://www.github.com/snakemake/snakemake-wrappers/commit/5727f2d1369ee5afe5fe0f3e5a051f81e51b553a)) * autobump bio/fgbio/collectduplexseqmetrics ([#3084](https://www.github.com/snakemake/snakemake-wrappers/issues/3084)) ([339720c](https://www.github.com/snakemake/snakemake-wrappers/commit/339720c78b04d1b407b171b099f0cbfdba4bf824)) * autobump bio/fgbio/filterconsensusreads ([#3086](https://www.github.com/snakemake/snakemake-wrappers/issues/3086)) ([1240b48](https://www.github.com/snakemake/snakemake-wrappers/commit/1240b481c4490f698fe1496cb5e129062caac2ed)) * autobump bio/fgbio/groupreadsbyumi ([#3083](https://www.github.com/snakemake/snakemake-wrappers/issues/3083)) ([333fcdd](https://www.github.com/snakemake/snakemake-wrappers/commit/333fcdd36475f410945eac1d9ba882df0693a542)) * autobump bio/fgbio/setmateinformation ([#3088](https://www.github.com/snakemake/snakemake-wrappers/issues/3088)) ([f9d678d](https://www.github.com/snakemake/snakemake-wrappers/commit/f9d678d51e1e81e1226f87432b98b510cd70901b)) * autobump bio/freebayes ([#3087](https://www.github.com/snakemake/snakemake-wrappers/issues/3087)) ([b23c95d](https://www.github.com/snakemake/snakemake-wrappers/commit/b23c95d9d12182f4e6234486b7ce4274272fa8be)) * autobump bio/gdc-api/bam-slicing ([#3089](https://www.github.com/snakemake/snakemake-wrappers/issues/3089)) ([5de2293](https://www.github.com/snakemake/snakemake-wrappers/commit/5de22930fe0f9fd6e8350bea5000a2c9b50d10d7)) * autobump bio/nonpareil/infer ([#3092](https://www.github.com/snakemake/snakemake-wrappers/issues/3092)) ([9e1cc99](https://www.github.com/snakemake/snakemake-wrappers/commit/9e1cc9914508fe883d4bfca064282b36fc1399f5)) * autobump bio/nonpareil/plot ([#3093](https://www.github.com/snakemake/snakemake-wrappers/issues/3093)) ([4b46579](https://www.github.com/snakemake/snakemake-wrappers/commit/4b465798b021e179830bc2ed980f4a5c194fcba2)) * autobump bio/taxonkit ([#3094](https://www.github.com/snakemake/snakemake-wrappers/issues/3094)) ([6046793](https://www.github.com/snakemake/snakemake-wrappers/commit/60467935840ff3e25cb40c7e16b106ce0fb8b64d)) * autobump bio/ucsc/gtfToGenePred ([#3095](https://www.github.com/snakemake/snakemake-wrappers/issues/3095)) ([1a4ddaa](https://www.github.com/snakemake/snakemake-wrappers/commit/1a4ddaade208efed101fb66ba9bb398946f7e807)) * autobump bio/unicycler ([#2987](https://www.github.com/snakemake/snakemake-wrappers/issues/2987)) ([a192628](https://www.github.com/snakemake/snakemake-wrappers/commit/a192628ce9523c0c0523e619571c3ca050187dca)) * Update Datavzrd wrapper ([#3074](https://www.github.com/snakemake/snakemake-wrappers/issues/3074)) ([9d47dd7](https://www.github.com/snakemake/snakemake-wrappers/commit/9d47dd76995e4baeb2b9ea7b3278cc713e9e4f17)) --- This PR was generated with [Release Please](https://github.com/googleapis/release-please). See [documentation](https://github.com/googleapis/release-please#release-please). Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> --- CHANGELOG.md | 29 +++++++++++++++++++++++++++++ 1 file changed, 29 insertions(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 6fa9d9b996d..477b6f9a13f 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -1,5 +1,34 @@ # Changelog +## [3.14.0](https://www.github.com/snakemake/snakemake-wrappers/compare/v3.13.8...v3.14.0) (2024-07-31) + + +### Features + +* add new wrapper to create annotation tables via Ensembl biomart ([#3072](https://www.github.com/snakemake/snakemake-wrappers/issues/3072)) ([07dc088](https://www.github.com/snakemake/snakemake-wrappers/commit/07dc08890bea0c13056d70f17a247f46c99e00ab)) + + +### Performance Improvements + +* autobump bio/blast/blastn ([#3080](https://www.github.com/snakemake/snakemake-wrappers/issues/3080)) ([bc0b80d](https://www.github.com/snakemake/snakemake-wrappers/commit/bc0b80db175c25a04cc2c4a3cd665f6be297741b)) +* autobump bio/blast/makeblastdb ([#3078](https://www.github.com/snakemake/snakemake-wrappers/issues/3078)) ([86ec876](https://www.github.com/snakemake/snakemake-wrappers/commit/86ec8769ddb9a881ca28d0b4600e24b5f9d41229)) +* autobump bio/bwa/mem ([#3079](https://www.github.com/snakemake/snakemake-wrappers/issues/3079)) ([01dc16f](https://www.github.com/snakemake/snakemake-wrappers/commit/01dc16fdebfab3ee6f36983a317fc8ea731f1d44)) +* autobump bio/entrez/efetch ([#3081](https://www.github.com/snakemake/snakemake-wrappers/issues/3081)) ([f178d5f](https://www.github.com/snakemake/snakemake-wrappers/commit/f178d5f1da9a8f420a1e1f8f08053f3983dc11e0)) +* autobump bio/fgbio/annotatebamwithumis ([#3082](https://www.github.com/snakemake/snakemake-wrappers/issues/3082)) ([b902adf](https://www.github.com/snakemake/snakemake-wrappers/commit/b902adfb65d0ea18dc557b25aa98031a394a99c8)) +* autobump bio/fgbio/callmolecularconsensusreads ([#3085](https://www.github.com/snakemake/snakemake-wrappers/issues/3085)) ([5727f2d](https://www.github.com/snakemake/snakemake-wrappers/commit/5727f2d1369ee5afe5fe0f3e5a051f81e51b553a)) +* autobump bio/fgbio/collectduplexseqmetrics ([#3084](https://www.github.com/snakemake/snakemake-wrappers/issues/3084)) ([339720c](https://www.github.com/snakemake/snakemake-wrappers/commit/339720c78b04d1b407b171b099f0cbfdba4bf824)) +* autobump bio/fgbio/filterconsensusreads ([#3086](https://www.github.com/snakemake/snakemake-wrappers/issues/3086)) ([1240b48](https://www.github.com/snakemake/snakemake-wrappers/commit/1240b481c4490f698fe1496cb5e129062caac2ed)) +* autobump bio/fgbio/groupreadsbyumi ([#3083](https://www.github.com/snakemake/snakemake-wrappers/issues/3083)) ([333fcdd](https://www.github.com/snakemake/snakemake-wrappers/commit/333fcdd36475f410945eac1d9ba882df0693a542)) +* autobump bio/fgbio/setmateinformation ([#3088](https://www.github.com/snakemake/snakemake-wrappers/issues/3088)) ([f9d678d](https://www.github.com/snakemake/snakemake-wrappers/commit/f9d678d51e1e81e1226f87432b98b510cd70901b)) +* autobump bio/freebayes ([#3087](https://www.github.com/snakemake/snakemake-wrappers/issues/3087)) ([b23c95d](https://www.github.com/snakemake/snakemake-wrappers/commit/b23c95d9d12182f4e6234486b7ce4274272fa8be)) +* autobump bio/gdc-api/bam-slicing ([#3089](https://www.github.com/snakemake/snakemake-wrappers/issues/3089)) ([5de2293](https://www.github.com/snakemake/snakemake-wrappers/commit/5de22930fe0f9fd6e8350bea5000a2c9b50d10d7)) +* autobump bio/nonpareil/infer ([#3092](https://www.github.com/snakemake/snakemake-wrappers/issues/3092)) ([9e1cc99](https://www.github.com/snakemake/snakemake-wrappers/commit/9e1cc9914508fe883d4bfca064282b36fc1399f5)) +* autobump bio/nonpareil/plot ([#3093](https://www.github.com/snakemake/snakemake-wrappers/issues/3093)) ([4b46579](https://www.github.com/snakemake/snakemake-wrappers/commit/4b465798b021e179830bc2ed980f4a5c194fcba2)) +* autobump bio/taxonkit ([#3094](https://www.github.com/snakemake/snakemake-wrappers/issues/3094)) ([6046793](https://www.github.com/snakemake/snakemake-wrappers/commit/60467935840ff3e25cb40c7e16b106ce0fb8b64d)) +* autobump bio/ucsc/gtfToGenePred ([#3095](https://www.github.com/snakemake/snakemake-wrappers/issues/3095)) ([1a4ddaa](https://www.github.com/snakemake/snakemake-wrappers/commit/1a4ddaade208efed101fb66ba9bb398946f7e807)) +* autobump bio/unicycler ([#2987](https://www.github.com/snakemake/snakemake-wrappers/issues/2987)) ([a192628](https://www.github.com/snakemake/snakemake-wrappers/commit/a192628ce9523c0c0523e619571c3ca050187dca)) +* Update Datavzrd wrapper ([#3074](https://www.github.com/snakemake/snakemake-wrappers/issues/3074)) ([9d47dd7](https://www.github.com/snakemake/snakemake-wrappers/commit/9d47dd76995e4baeb2b9ea7b3278cc713e9e4f17)) + ### [3.13.8](https://www.github.com/snakemake/snakemake-wrappers/compare/v3.13.7...v3.13.8) (2024-07-18) From 248b611f33ce879ad40eef4b78ad2d84cda43948 Mon Sep 17 00:00:00 2001 From: "snakedeploy-bot[bot]" <115615832+snakedeploy-bot[bot]@users.noreply.github.com> Date: Fri, 2 Aug 2024 03:12:03 +0000 Subject: [PATCH 24/62] perf: autobump bio/gdc-api/bam-slicing (#3096) Automatic bump of bio/gdc-api/bam-slicing. --------- Co-authored-by: snakedeploy-bot[bot] <115615832+snakedeploy-bot[bot]@users.noreply.github.com> --- bio/gdc-api/bam-slicing/environment.linux-64.pin.txt | 4 ++-- bio/gdc-api/bam-slicing/environment.yaml | 2 +- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/bio/gdc-api/bam-slicing/environment.linux-64.pin.txt b/bio/gdc-api/bam-slicing/environment.linux-64.pin.txt index bb2c4eb472f..4b8e820964a 100644 --- a/bio/gdc-api/bam-slicing/environment.linux-64.pin.txt +++ b/bio/gdc-api/bam-slicing/environment.linux-64.pin.txt @@ -19,5 +19,5 @@ https://conda.anaconda.org/conda-forge/linux-64/libnghttp2-1.58.0-h47da74e_1.con https://conda.anaconda.org/conda-forge/linux-64/libssh2-1.11.0-h0841786_0.conda#1f5a58e686b13bcfde88b93f547d23fe https://conda.anaconda.org/conda-forge/linux-64/zstd-1.5.6-ha6fb4c9_0.conda#4d056880988120e29d75bfff282e0f45 https://conda.anaconda.org/conda-forge/linux-64/krb5-1.21.3-h659f571_0.conda#3f43953b7d3fb3aaa1d0d0723d91e368 -https://conda.anaconda.org/conda-forge/linux-64/libcurl-8.9.0-hdb1bdb2_0.conda#5badfbdb2688d8aaca7bd3c98d557b97 -https://conda.anaconda.org/conda-forge/linux-64/curl-8.9.0-h18eb788_0.conda#cb385c8a955ad49c3342b23cd1a26c11 +https://conda.anaconda.org/conda-forge/linux-64/libcurl-8.9.1-hdb1bdb2_0.conda#7da1d242ca3591e174a3c7d82230d3c0 +https://conda.anaconda.org/conda-forge/linux-64/curl-8.9.1-h18eb788_0.conda#2e7dedf73dfbfcee662e2a0f6175e4bb diff --git a/bio/gdc-api/bam-slicing/environment.yaml b/bio/gdc-api/bam-slicing/environment.yaml index 0371dd78aaf..ca425b5199c 100644 --- a/bio/gdc-api/bam-slicing/environment.yaml +++ b/bio/gdc-api/bam-slicing/environment.yaml @@ -2,4 +2,4 @@ channels: - conda-forge - nodefaults dependencies: - - curl =8.9.0 + - curl =8.9.1 From 5796bc6fe0908c4922bb8bfc93183df72afa04b2 Mon Sep 17 00:00:00 2001 From: "snakedeploy-bot[bot]" <115615832+snakedeploy-bot[bot]@users.noreply.github.com> Date: Fri, 2 Aug 2024 04:51:04 +0000 Subject: [PATCH 25/62] perf: autobump bio/sourmash/compute (#3098) Automatic bump of bio/sourmash/compute. --------- Co-authored-by: snakedeploy-bot[bot] <115615832+snakedeploy-bot[bot]@users.noreply.github.com> --- .../compute/environment.linux-64.pin.txt | 32 +++++++++---------- bio/sourmash/compute/environment.yaml | 2 +- 2 files changed, 17 insertions(+), 17 deletions(-) diff --git a/bio/sourmash/compute/environment.linux-64.pin.txt b/bio/sourmash/compute/environment.linux-64.pin.txt index a8991000809..8ec4d86dcd7 100644 --- a/bio/sourmash/compute/environment.linux-64.pin.txt +++ b/bio/sourmash/compute/environment.linux-64.pin.txt @@ -10,7 +10,7 @@ https://conda.anaconda.org/conda-forge/noarch/tzdata-2024a-h0c530f3_0.conda#1610 https://conda.anaconda.org/conda-forge/linux-64/libgomp-14.1.0-h77fa898_0.conda#ae061a5ed5f05818acdf9adab72c146d https://conda.anaconda.org/conda-forge/linux-64/_openmp_mutex-4.5-2_gnu.tar.bz2#73aaf86a425cc6e73fcf236a5a46396d https://conda.anaconda.org/conda-forge/linux-64/libgcc-ng-14.1.0-h77fa898_0.conda#ca0fad6a41ddaef54a153b78eccb5037 -https://conda.anaconda.org/conda-forge/linux-64/bzip2-1.0.8-hd590300_5.conda#69b8b6202a07720f448be700e300ccf4 +https://conda.anaconda.org/conda-forge/linux-64/bzip2-1.0.8-h4bc722e_7.conda#62ee74e96c5ebb0af99386de58cf9553 https://conda.anaconda.org/conda-forge/linux-64/libbrotlicommon-1.1.0-hd590300_1.conda#aec6c91c7371c26392a06708a73c70e5 https://conda.anaconda.org/conda-forge/linux-64/libdeflate-1.20-hd590300_0.conda#8e88f9389f1165d7c0936fe40d9a9a79 https://conda.anaconda.org/conda-forge/linux-64/libexpat-2.6.2-h59595ed_0.conda#e7ba12deb7020dd080c6c70e7b6f6a3d @@ -24,7 +24,7 @@ https://conda.anaconda.org/conda-forge/linux-64/libwebp-base-1.4.0-hd590300_0.co https://conda.anaconda.org/conda-forge/linux-64/libxcrypt-4.4.36-hd590300_1.conda#5aa797f8787fe7a17d1b0821485b5adc https://conda.anaconda.org/conda-forge/linux-64/libzlib-1.3.1-h4ab18f5_1.conda#57d7dc60e9325e3de37ff8dffd18e814 https://conda.anaconda.org/conda-forge/linux-64/ncurses-6.5-h59595ed_0.conda#fcea371545eda051b6deafb24889fc69 -https://conda.anaconda.org/conda-forge/linux-64/openssl-3.3.1-h4ab18f5_1.conda#b1e9d076f14e8d776213fd5047b4c3d9 +https://conda.anaconda.org/conda-forge/linux-64/openssl-3.3.1-h4bc722e_2.conda#e1b454497f9f7c1147fdde4b53f1b512 https://conda.anaconda.org/conda-forge/linux-64/pthread-stubs-0.4-h36c2ea0_1001.tar.bz2#22dad4df6e8630e8dff2428f6f6a7036 https://conda.anaconda.org/conda-forge/linux-64/xorg-libxau-1.0.11-hd590300_0.conda#2c80dc38fface310c9bd81b17037fee5 https://conda.anaconda.org/conda-forge/linux-64/xorg-libxdmcp-1.1.3-h7f98852_0.tar.bz2#be93aabceefa2fac576e971aef407908 @@ -36,43 +36,43 @@ https://conda.anaconda.org/conda-forge/linux-64/libgfortran-ng-14.1.0-h69a702a_0 https://conda.anaconda.org/conda-forge/linux-64/libpng-1.6.43-h2797004_0.conda#009981dd9cfcaa4dbfa25ffaed86bcae https://conda.anaconda.org/conda-forge/linux-64/libsqlite-3.46.0-hde9e2c9_0.conda#18aa975d2094c34aef978060ae7da7d8 https://conda.anaconda.org/conda-forge/linux-64/libxcb-1.16-hd590300_0.conda#151cba22b85a989c2d6ef9633ffee1e4 -https://conda.anaconda.org/conda-forge/linux-64/qhull-2020.2-h4bd325d_2.tar.bz2#5acb8407fefa1c1929c11c167237e776 +https://conda.anaconda.org/conda-forge/linux-64/qhull-2020.2-h434a139_5.conda#353823361b1d27eb3960efb076dfcaf6 https://conda.anaconda.org/conda-forge/linux-64/readline-8.2-h8228510_1.conda#47d31b792659ce70f470b5c82fdfb7a4 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-https://conda.anaconda.org/conda-forge/linux-64/numpy-2.0.0-py312h22e1c76_0.conda#7956c7d65f87aecaba720af6088e72c3 +https://conda.anaconda.org/conda-forge/linux-64/numpy-2.0.1-py312h1103770_0.conda#9f444595d8d9682891f2f078fc19da43 https://conda.anaconda.org/conda-forge/linux-64/contourpy-1.2.1-py312h8572e83_0.conda#12c6a831ef734f0b2dd4caff514cbb7f -https://conda.anaconda.org/conda-forge/linux-64/scipy-1.14.0-py312hc2bc53b_0.conda#d526782bc49958ab75fe6fb505647b54 -https://conda.anaconda.org/conda-forge/linux-64/matplotlib-base-3.9.0-py312h9201f00_0.conda#7bb82ac36ec29595c2a659099fca1a88 -https://conda.anaconda.org/conda-forge/linux-64/sourmash-minimal-4.8.10-py312h5a5b059_0.conda#10da82160e19402b0a6898d8d6d88d3c -https://conda.anaconda.org/bioconda/noarch/sourmash-4.8.10-hdfd78af_0.tar.bz2#172eefbb692c84c978e821a58ccccfc0 +https://conda.anaconda.org/conda-forge/linux-64/scipy-1.14.0-py312hc2bc53b_1.conda#eae80145f63aa04a02dda456d4883b46 +https://conda.anaconda.org/conda-forge/linux-64/matplotlib-base-3.9.1-py312h854627b_1.conda#3e91b5c827934aae7a6694e3aa41cc27 +https://conda.anaconda.org/conda-forge/linux-64/sourmash-minimal-4.8.11-py312h7703976_0.conda#4d61747ee9b83d017314d733f7730dc1 +https://conda.anaconda.org/bioconda/noarch/sourmash-4.8.11-hdfd78af_0.tar.bz2#19975443e4707c1a0cc80454fe30afb9 diff --git a/bio/sourmash/compute/environment.yaml b/bio/sourmash/compute/environment.yaml index f9508785a61..03954a39344 100644 --- a/bio/sourmash/compute/environment.yaml +++ b/bio/sourmash/compute/environment.yaml @@ -3,4 +3,4 @@ channels: - bioconda - nodefaults dependencies: - - sourmash =4.8.10 + - sourmash =4.8.11 From a09832ae1ada3771d130087bc6dec5656b635643 Mon Sep 17 00:00:00 2001 From: "snakedeploy-bot[bot]" <115615832+snakedeploy-bot[bot]@users.noreply.github.com> Date: Fri, 2 Aug 2024 05:16:09 +0000 Subject: [PATCH 26/62] perf: autobump bio/unicycler (#3099) Automatic bump of bio/unicycler. --------- Co-authored-by: snakedeploy-bot[bot] <115615832+snakedeploy-bot[bot]@users.noreply.github.com> --- bio/unicycler/environment.linux-64.pin.txt | 18 ++++++++---------- bio/unicycler/environment.yaml | 2 +- 2 files changed, 9 insertions(+), 11 deletions(-) diff --git a/bio/unicycler/environment.linux-64.pin.txt b/bio/unicycler/environment.linux-64.pin.txt index 1edc555c4e0..62667095b60 100644 --- a/bio/unicycler/environment.linux-64.pin.txt +++ b/bio/unicycler/environment.linux-64.pin.txt @@ -67,7 +67,6 @@ https://conda.anaconda.org/conda-forge/linux-64/libpng-1.6.43-h2797004_0.conda#0 https://conda.anaconda.org/conda-forge/linux-64/libsqlite-3.46.0-hde9e2c9_0.conda#18aa975d2094c34aef978060ae7da7d8 https://conda.anaconda.org/conda-forge/linux-64/libssh2-1.11.0-h0841786_0.conda#1f5a58e686b13bcfde88b93f547d23fe https://conda.anaconda.org/conda-forge/linux-64/libxcb-1.16-hd590300_0.conda#151cba22b85a989c2d6ef9633ffee1e4 -https://conda.anaconda.org/conda-forge/linux-64/llvm-openmp-8.0.1-hc9558a2_0.tar.bz2#67590caab043d6d7ffc371f9cced7848 https://conda.anaconda.org/bioconda/linux-64/ncbi-vdb-3.1.1-h4ac6f70_1.tar.bz2#05705db906896430d0d963de7a3c1698 https://conda.anaconda.org/conda-forge/linux-64/pcre-8.45-h9c3ff4c_0.tar.bz2#c05d1820a6d34ff07aaaab7a9b7eddaa https://conda.anaconda.org/conda-forge/linux-64/pcre2-10.44-h0f59acf_0.conda#3914f7ac1761dce57102c72ca7c35d01 @@ -87,7 +86,6 @@ https://conda.anaconda.org/conda-forge/linux-64/libopenblas-0.3.27-pthreads_hac2 https://conda.anaconda.org/conda-forge/linux-64/libtiff-4.6.0-h1dd3fc0_3.conda#66f03896ffbe1a110ffda05c7a856504 https://conda.anaconda.org/conda-forge/linux-64/libxml2-2.12.7-he7c6b58_4.conda#08a9265c637230c37cb1be4a6cad4536 https://conda.anaconda.org/bioconda/linux-64/miniasm-0.2-0.tar.bz2#842e7e7c3557e66bd5467c72e0c3e3e3 -https://conda.anaconda.org/conda-forge/linux-64/openmp-8.0.1-0.tar.bz2#b35241079152e5cc891c99368395b2c6 https://conda.anaconda.org/conda-forge/noarch/perl-common-sense-3.75-pl5321hd8ed1ab_0.tar.bz2#ef70dc77e8b10bbb62f5e843b401ef0e https://conda.anaconda.org/conda-forge/linux-64/perl-compress-raw-bzip2-2.201-pl5321h166bdaf_0.tar.bz2#105e211458bf45fe64b6de5ae8283ba4 https://conda.anaconda.org/conda-forge/linux-64/perl-compress-raw-zlib-2.202-pl5321h166bdaf_0.tar.bz2#66176366c49e2f70b3a764bc744b5010 @@ -106,7 +104,7 @@ https://conda.anaconda.org/conda-forge/linux-64/gettext-0.22.5-h59595ed_2.conda# https://conda.anaconda.org/conda-forge/linux-64/lcms2-2.16-hb7c19ff_0.conda#51bb7010fc86f70eee639b4bb7a894f5 https://conda.anaconda.org/conda-forge/linux-64/libblas-3.9.0-23_linux64_openblas.conda#96c8450a40aa2b9733073a9460de972c https://conda.anaconda.org/conda-forge/linux-64/libcups-2.3.3-h4637d8d_4.conda#d4529f4dff3057982a7617c7ac58fde3 -https://conda.anaconda.org/conda-forge/linux-64/libcurl-8.9.0-hdb1bdb2_0.conda#5badfbdb2688d8aaca7bd3c98d557b97 +https://conda.anaconda.org/conda-forge/linux-64/libcurl-8.9.1-hdb1bdb2_0.conda#7da1d242ca3591e174a3c7d82230d3c0 https://conda.anaconda.org/conda-forge/linux-64/libhwloc-2.11.1-default_hecaa2ac_1000.conda#f54aeebefb5c5ff84eca4fb05ca8aa3a https://conda.anaconda.org/conda-forge/noarch/perl-carp-1.50-pl5321hd8ed1ab_0.tar.bz2#bdddc03e28019b902da71b722f2288d7 https://conda.anaconda.org/conda-forge/linux-64/perl-encode-3.21-pl5321hd590300_0.conda#704fb52dc57c97cf5adcc057c8b40a0a @@ -114,28 +112,28 @@ https://conda.anaconda.org/bioconda/noarch/perl-list-moreutils-0.430-pl5321hdfd7 https://conda.anaconda.org/bioconda/noarch/perl-types-serialiser-1.01-pl5321hdfd78af_0.tar.bz2#cfc65753e827bbef80c00eaa395f6ae7 https://conda.anaconda.org/bioconda/linux-64/racon-1.5.0-hdcf5f25_4.tar.bz2#bd536e372f360a37b1820e34024ea377 https://conda.anaconda.org/conda-forge/noarch/setuptools-71.0.4-pyhd8ed1ab_0.conda#ee78ac9c720d0d02fcfd420866b82ab1 -https://conda.anaconda.org/bioconda/linux-64/spades-3.15.5-h5fb382e_3.tar.bz2#979669ff13b1f1b8b53167873ada2f69 +https://conda.anaconda.org/bioconda/linux-64/spades-4.0.0-h5fb382e_2.tar.bz2#a022789b131c832c2a564cea8b5c8822 https://conda.anaconda.org/conda-forge/noarch/wheel-0.43.0-pyhd8ed1ab_1.conda#0b5293a157c2b5cd513dd1b03d8d3aae https://conda.anaconda.org/conda-forge/linux-64/xorg-libxext-1.3.4-h0b41bf4_2.conda#82b6df12252e6f32402b96dacc656fec https://conda.anaconda.org/conda-forge/linux-64/xorg-libxfixes-5.0.3-h7f98852_1004.tar.bz2#e9a21aa4d5e3e5f1aed71e8cefd46b6a https://conda.anaconda.org/conda-forge/linux-64/xorg-libxrender-0.9.11-hd590300_0.conda#ed67c36f215b310412b2af935bf3e530 https://conda.anaconda.org/conda-forge/linux-64/xorg-libxt-1.3.0-hd590300_1.conda#ae92aab42726eb29d16488924f7312cb https://conda.anaconda.org/conda-forge/linux-64/cairo-1.18.0-hebfffa5_3.conda#fceaedf1cdbcb02df9699a0d9b005292 -https://conda.anaconda.org/conda-forge/linux-64/curl-8.9.0-h18eb788_0.conda#cb385c8a955ad49c3342b23cd1a26c11 +https://conda.anaconda.org/conda-forge/linux-64/curl-8.9.1-h18eb788_0.conda#2e7dedf73dfbfcee662e2a0f6175e4bb https://conda.anaconda.org/bioconda/linux-64/htslib-1.20-h5efdd21_2.tar.bz2#f0923cdb85b44dc77bdead8018645ea9 https://conda.anaconda.org/conda-forge/linux-64/libcblas-3.9.0-23_linux64_openblas.conda#eede29b40efa878cbe5bdcb767e97310 https://conda.anaconda.org/conda-forge/linux-64/libidn2-2.3.7-hd590300_0.conda#2b7b0d827c6447cc1d85dc06d5b5de46 https://conda.anaconda.org/bioconda/linux-64/perl-io-compress-2.201-pl5321hdbdd923_2.tar.bz2#f40f599ce37ad75715bab686baa08197 -https://conda.anaconda.org/bioconda/linux-64/perl-json-xs-2.34-pl5321h4ac6f70_6.tar.bz2#e01a73e25a790b129920f9e663e4935f +https://conda.anaconda.org/bioconda/linux-64/perl-json-xs-4.03-pl5321h4ac6f70_3.tar.bz2#7916cbb7315bc05abbaa0c383d379964 https://conda.anaconda.org/conda-forge/linux-64/perl-pathtools-3.75-pl5321h166bdaf_0.tar.bz2#4e72abd06ec15cb28c14798dab2c10c8 -https://conda.anaconda.org/conda-forge/noarch/pip-24.0-pyhd8ed1ab_0.conda#f586ac1e56c8638b64f9c8122a7b8a67 +https://conda.anaconda.org/conda-forge/noarch/pip-24.2-pyhd8ed1ab_0.conda#6721aef6bfe5937abe70181545dd2c51 https://conda.anaconda.org/conda-forge/linux-64/tbb-2021.12.0-h434a139_3.conda#c667c11d1e488a38220ede8a34441bff -https://conda.anaconda.org/conda-forge/linux-64/xorg-libxi-1.7.10-h7f98852_0.tar.bz2#e77615e5141cad5a2acaa043d1cf0ca5 +https://conda.anaconda.org/conda-forge/linux-64/xorg-libxi-1.7.10-h4bc722e_1.conda#749baebe7e2ff3360630e069175e528b https://conda.anaconda.org/bioconda/linux-64/bowtie2-2.5.4-he20e202_2.tar.bz2#a4265d59f9fc5dda22130c0c6bdd6c3c https://conda.anaconda.org/conda-forge/linux-64/gsl-2.7-he838d99_0.tar.bz2#fec079ba39c9cca093bf4c00001825de https://conda.anaconda.org/conda-forge/linux-64/harfbuzz-9.0.0-hda332d3_1.conda#76b32dcf243444aea9c6b804bcfa40b8 https://conda.anaconda.org/bioconda/noarch/perl-archive-tar-2.40-pl5321hdfd78af_0.tar.bz2#ef5f007762b5ad9425694104d7db4463 -https://conda.anaconda.org/bioconda/noarch/perl-json-4.10-pl5321hdfd78af_0.tar.bz2#05467eeb1e57206d8dddf31c3128cd00 +https://conda.anaconda.org/bioconda/noarch/perl-json-4.10-pl5321hdfd78af_1.tar.bz2#c6c43c11e14d90b836f42c611e106ea9 https://conda.anaconda.org/bioconda/linux-64/samtools-1.20-h50ea8bc_1.tar.bz2#1a4c52f8079fea1b18b3e4bd329bab3a https://conda.anaconda.org/conda-forge/linux-64/wget-1.21.4-hda4d442_0.conda#361e96b664eac64a33c20dfd11affbff https://conda.anaconda.org/conda-forge/linux-64/xorg-libxtst-1.2.4-h4bc722e_0.conda#4561491e71d04bfe58d4f0ce5329656e @@ -144,4 +142,4 @@ https://conda.anaconda.org/bioconda/linux-64/entrez-direct-22.4-he881be0_0.tar.b https://conda.anaconda.org/conda-forge/linux-64/openjdk-22.0.1-h8651b0f_1.conda#672153e7c3d4f70bc65993f3ee513768 https://conda.anaconda.org/bioconda/linux-64/blast-2.16.0-h6f7f691_0.tar.bz2#098092890e9c94de10a3fe827339bc16 https://conda.anaconda.org/bioconda/noarch/pilon-1.24-hdfd78af_0.tar.bz2#4eef0c771dd3f81effb0d21ba8bb6734 -https://conda.anaconda.org/bioconda/linux-64/unicycler-0.5.1-py312hc60241a_0.tar.bz2#e7e6c365185bed6ecdad294a3ce160e8 +https://conda.anaconda.org/bioconda/linux-64/unicycler-0.5.1-py312hc60241a_1.tar.bz2#968b436f2872899bf82c980c2470c15e diff --git a/bio/unicycler/environment.yaml b/bio/unicycler/environment.yaml index 7c3e106624c..ffce1f9c86c 100644 --- a/bio/unicycler/environment.yaml +++ b/bio/unicycler/environment.yaml @@ -5,7 +5,7 @@ channels: dependencies: - bowtie2 =2.5.4 - bcftools =1.20 - - spades =3.15.5 + - spades =4.0.0 - samtools =1.20 - pilon =1.24 - racon =1.5.0 From 13c6ef74db8f6c4608c87f6209bab69b3e9ed16a Mon Sep 17 00:00:00 2001 From: Till Hartmann Date: Tue, 6 Aug 2024 14:09:52 +0200 Subject: [PATCH 27/62] fix: download already indexed vep cache tarball (#3102) This PR adds a parameter named `indexed` to the wrapper interface to allow downloading a vep_cache version which has already been indexed and thus needs no additional post-processing via `--CONVERT`. > Tabix-indexed cache files are available to download for most supported species in our [FTP server](https://ftp.ensembl.org/pub/release-112/variation/indexed_vep_cache/). [[1]](http://www.ensembl.org/info/docs/tools/vep/script/vep_cache.html) ### QC * [x] I confirm that I have followed the [documentation for contributing to `snakemake-wrappers`](https://snakemake-wrappers.readthedocs.io/en/stable/contributing.html). While the contributions guidelines are more extensive, please particularly ensure that: * [x] `test.py` was updated to call any added or updated example rules in a `Snakefile` * [x] `input:` and `output:` file paths in the rules can be chosen arbitrarily * [x] wherever possible, command line arguments are inferred and set automatically (e.g. based on file extensions in `input:` or `output:`) * [x] temporary files are either written to a unique hidden folder in the working directory, or (better) stored where the Python function `tempfile.gettempdir()` points to * [x] the `meta.yaml` contains a link to the documentation of the respective tool or command under `url:` * [x] conda environments use a minimal amount of channels and packages, in recommended ordering --- bio/vep/cache/meta.yaml | 1 + bio/vep/cache/test/Snakefile | 15 +++++++++++++++ bio/vep/cache/wrapper.py | 9 +++++++-- test.py | 5 +++++ 4 files changed, 28 insertions(+), 2 deletions(-) diff --git a/bio/vep/cache/meta.yaml b/bio/vep/cache/meta.yaml index 220cec2c1f6..899c722aae7 100644 --- a/bio/vep/cache/meta.yaml +++ b/bio/vep/cache/meta.yaml @@ -10,3 +10,4 @@ params: - species: species to download cache data - build: build to download cache data - release: release to download cache data + - indexed: whether to download an already indexed cache diff --git a/bio/vep/cache/test/Snakefile b/bio/vep/cache/test/Snakefile index c2666c9547b..65c3a88129f 100644 --- a/bio/vep/cache/test/Snakefile +++ b/bio/vep/cache/test/Snakefile @@ -12,6 +12,21 @@ rule get_vep_cache: "master/bio/vep/cache" +rule get_indexed_vep_cache: + output: + directory("resources/vep/indexed_cache"), + params: + species="saccharomyces_cerevisiae", + build="R64-1-1", + release="98", + indexed=True, + log: + "logs/vep/indexed_cache.log", + cache: "omit-software" # save space and time with between workflow caching (see docs) + wrapper: + "master/bio/vep/cache" + + rule get_vep_cache_ebi: output: directory("resources/vep/cache_ebi"), diff --git a/bio/vep/cache/wrapper.py b/bio/vep/cache/wrapper.py index 291d8161210..d1400b7aedd 100644 --- a/bio/vep/cache/wrapper.py +++ b/bio/vep/cache/wrapper.py @@ -25,7 +25,12 @@ cache_tarball = ( f"{snakemake.params.species}_vep_{release}_{snakemake.params.build}.tar.gz" ) - vep_dir = "vep" if snakemake.params.get("url") or release >= 97 else "VEP" + if snakemake.params.get("indexed"): + vep_dir = "indexed_vep_cache" + convert = "" + else: + vep_dir = "vep" if snakemake.params.get("url") or release >= 97 else "VEP" + convert = "--CONVERT " shell( "curl -L {cache_url}/release-{release}/variation/{vep_dir}/{cache_tarball} -o {tmpdir}/{cache_tarball} {log}" ) @@ -38,7 +43,7 @@ "--CACHE_VERSION {release} " "--CACHEURL {tmpdir} " "--CACHEDIR {snakemake.output} " - "--CONVERT " + "{convert}" "--NO_UPDATE " "{extra} {log}" ) diff --git a/test.py b/test.py index 11b81bd6db3..cbf1f32e83c 100644 --- a/test.py +++ b/test.py @@ -6088,6 +6088,11 @@ def test_vep_cache(): ["snakemake", "--cores", "1", "resources/vep/cache", "--use-conda", "-F"], ) + run( + "bio/vep/cache", + ["snakemake", "--cores", "1", "resources/vep/indexed_cache", "--use-conda", "-F"], + ) + run( "bio/vep/cache", ["snakemake", "--cores", "1", "resources/vep/cache_ebi", "--use-conda", "-F"], From 74a3269fe7152464e8134d7560a32540e4197977 Mon Sep 17 00:00:00 2001 From: Markus Riedl <50179943+mriedl93@users.noreply.github.com> Date: Thu, 8 Aug 2024 11:52:38 +0200 Subject: [PATCH 28/62] fix: add missing raw string in REGEX_RULES (#3104) I ran into an error while trying to use the trim_galore/pe wrapper: ``` /path/to/project/.snakemake/scripts/tmph05pgi_u.wrapper.py:38: SyntaxWarning: invalid escape sequence '\.' REGEX_RULES = [r"\.fastq$", "\.fastq\.gz$", r"\.fq$", r"\.fq\.gz$"] ``` The fix for that issue was easy and obvious, I fixed the raw string for `.fastq.gz` files in the list of regex patterns. ### QC * [X] I confirm that I have followed the [documentation for contributing to `snakemake-wrappers`](https://snakemake-wrappers.readthedocs.io/en/stable/contributing.html). While the contributions guidelines are more extensive, please particularly ensure that: * [ ] `test.py` was updated to call any added or updated example rules in a `Snakefile` * [ ] `input:` and `output:` file paths in the rules can be chosen arbitrarily * [ ] wherever possible, command line arguments are inferred and set automatically (e.g. based on file extensions in `input:` or `output:`) * [ ] temporary files are either written to a unique hidden folder in the working directory, or (better) stored where the Python function `tempfile.gettempdir()` points to * [ ] the `meta.yaml` contains a link to the documentation of the respective tool or command under `url:` * [ ] conda environments use a minimal amount of channels and packages, in recommended ordering --- bio/trim_galore/pe/wrapper.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/bio/trim_galore/pe/wrapper.py b/bio/trim_galore/pe/wrapper.py index 801abb1c89e..827230da012 100644 --- a/bio/trim_galore/pe/wrapper.py +++ b/bio/trim_galore/pe/wrapper.py @@ -31,7 +31,7 @@ def fasta_filename(infile: str, infix: str, out_gzip: bool) -> str: """ base_input = os.path.basename(infile) suffix = ".gz" if out_gzip or infile.endswith(".gz") else "" - REGEX_RULES = [r"\.fastq$", "\.fastq\.gz$", r"\.fq$", r"\.fq\.gz$"] + REGEX_RULES = [r"\.fastq$", r"\.fastq\.gz$", r"\.fq$", r"\.fq\.gz$"] for regex in REGEX_RULES: if re.search(regex, base_input): return re.sub(regex, f"{infix}.fq", base_input) + suffix From 695ab1b1e39ec2a9693ef5f721bc564e50f716e2 Mon Sep 17 00:00:00 2001 From: "snakedeploy-bot[bot]" <115615832+snakedeploy-bot[bot]@users.noreply.github.com> Date: Fri, 9 Aug 2024 02:56:22 +0000 Subject: [PATCH 29/62] perf: autobump bio/encode_fastq_downloader (#3105) Automatic bump of bio/encode_fastq_downloader. --------- Co-authored-by: snakedeploy-bot[bot] <115615832+snakedeploy-bot[bot]@users.noreply.github.com> --- .../environment.linux-64.pin.txt | 18 +++++++++--------- bio/encode_fastq_downloader/environment.yaml | 2 +- 2 files changed, 10 insertions(+), 10 deletions(-) diff --git a/bio/encode_fastq_downloader/environment.linux-64.pin.txt b/bio/encode_fastq_downloader/environment.linux-64.pin.txt index 4b7d0003a50..13369a66521 100644 --- a/bio/encode_fastq_downloader/environment.linux-64.pin.txt +++ b/bio/encode_fastq_downloader/environment.linux-64.pin.txt @@ -3,13 +3,13 @@ # platform: linux-64 @EXPLICIT https://conda.anaconda.org/conda-forge/linux-64/_libgcc_mutex-0.1-conda_forge.tar.bz2#d7c89558ba9fa0495403155b64376d81 -https://conda.anaconda.org/conda-forge/linux-64/ca-certificates-2024.6.2-hbcca054_0.conda#847c3c2905cc467cea52c24f9cfa8080 +https://conda.anaconda.org/conda-forge/linux-64/ca-certificates-2024.7.4-hbcca054_0.conda#23ab7665c5f63cfb9f1f6195256daac6 https://conda.anaconda.org/conda-forge/linux-64/ld_impl_linux-64-2.40-hf3520f5_7.conda#b80f2f396ca2c28b8c14c437a4ed1e74 https://conda.anaconda.org/conda-forge/noarch/tzdata-2024a-h0c530f3_0.conda#161081fc7cec0bfda0d86d7cb595f8d8 -https://conda.anaconda.org/conda-forge/linux-64/libgomp-13.2.0-h77fa898_11.conda#8c462ced2af33648195dc9459f331f31 +https://conda.anaconda.org/conda-forge/linux-64/libgomp-14.1.0-h77fa898_0.conda#ae061a5ed5f05818acdf9adab72c146d https://conda.anaconda.org/conda-forge/linux-64/_openmp_mutex-4.5-2_gnu.tar.bz2#73aaf86a425cc6e73fcf236a5a46396d -https://conda.anaconda.org/conda-forge/linux-64/libgcc-ng-13.2.0-h77fa898_11.conda#0b3b218a596bb4c3854cc9ee799f94e5 -https://conda.anaconda.org/conda-forge/linux-64/bzip2-1.0.8-hd590300_5.conda#69b8b6202a07720f448be700e300ccf4 +https://conda.anaconda.org/conda-forge/linux-64/libgcc-ng-14.1.0-h77fa898_0.conda#ca0fad6a41ddaef54a153b78eccb5037 +https://conda.anaconda.org/conda-forge/linux-64/bzip2-1.0.8-h4bc722e_7.conda#62ee74e96c5ebb0af99386de58cf9553 https://conda.anaconda.org/conda-forge/linux-64/libexpat-2.6.2-h59595ed_0.conda#e7ba12deb7020dd080c6c70e7b6f6a3d https://conda.anaconda.org/conda-forge/linux-64/libffi-3.4.2-h7f98852_5.tar.bz2#d645c6d2ac96843a2bfaccd2d62b3ac3 https://conda.anaconda.org/conda-forge/linux-64/libnsl-2.0.1-hd590300_0.conda#30fd6e37fe21f86f4bd26d6ee73eeec7 @@ -17,12 +17,12 @@ https://conda.anaconda.org/conda-forge/linux-64/libuuid-2.38.1-h0b41bf4_0.conda# https://conda.anaconda.org/conda-forge/linux-64/libxcrypt-4.4.36-hd590300_1.conda#5aa797f8787fe7a17d1b0821485b5adc https://conda.anaconda.org/conda-forge/linux-64/libzlib-1.3.1-h4ab18f5_1.conda#57d7dc60e9325e3de37ff8dffd18e814 https://conda.anaconda.org/conda-forge/linux-64/ncurses-6.5-h59595ed_0.conda#fcea371545eda051b6deafb24889fc69 -https://conda.anaconda.org/conda-forge/linux-64/openssl-3.3.1-h4ab18f5_0.conda#a41fa0e391cc9e0d6b78ac69ca047a6c +https://conda.anaconda.org/conda-forge/linux-64/openssl-3.3.1-h4bc722e_2.conda#e1b454497f9f7c1147fdde4b53f1b512 https://conda.anaconda.org/conda-forge/linux-64/xz-5.2.6-h166bdaf_0.tar.bz2#2161070d867d1b1204ea749c8eec4ef0 https://conda.anaconda.org/conda-forge/linux-64/libsqlite-3.46.0-hde9e2c9_0.conda#18aa975d2094c34aef978060ae7da7d8 https://conda.anaconda.org/conda-forge/linux-64/readline-8.2-h8228510_1.conda#47d31b792659ce70f470b5c82fdfb7a4 https://conda.anaconda.org/conda-forge/linux-64/tk-8.6.13-noxft_h4845f30_101.conda#d453b98d9c83e71da0741bb0ff4d76bc -https://conda.anaconda.org/conda-forge/linux-64/python-3.12.4-h194c7f8_0_cpython.conda#d73490214f536cccb5819e9873048c92 -https://conda.anaconda.org/conda-forge/noarch/setuptools-70.1.0-pyhd8ed1ab_0.conda#258e66f95f814d51ada2a1fe9274039b -https://conda.anaconda.org/conda-forge/noarch/wheel-0.43.0-pyhd8ed1ab_1.conda#0b5293a157c2b5cd513dd1b03d8d3aae -https://conda.anaconda.org/conda-forge/noarch/pip-24.0-pyhd8ed1ab_0.conda#f586ac1e56c8638b64f9c8122a7b8a67 +https://conda.anaconda.org/conda-forge/linux-64/python-3.12.5-h2ad013b_0_cpython.conda#9c56c4df45f6571b13111d8df2448692 +https://conda.anaconda.org/conda-forge/noarch/setuptools-72.1.0-pyhd8ed1ab_0.conda#e06d4c26df4f958a8d38696f2c344d15 +https://conda.anaconda.org/conda-forge/noarch/wheel-0.44.0-pyhd8ed1ab_0.conda#d44e3b085abcaef02983c6305b84b584 +https://conda.anaconda.org/conda-forge/noarch/pip-24.2-pyhd8ed1ab_0.conda#6721aef6bfe5937abe70181545dd2c51 diff --git a/bio/encode_fastq_downloader/environment.yaml b/bio/encode_fastq_downloader/environment.yaml index 19c3d8cd50e..7bdf1ccaa85 100644 --- a/bio/encode_fastq_downloader/environment.yaml +++ b/bio/encode_fastq_downloader/environment.yaml @@ -3,4 +3,4 @@ channels: - bioconda - nodefaults dependencies: - - python =3.12.4 + - python =3.12.5 From 09d6e0b0d0857c88f6f2c81aec3d7714eb9fb738 Mon Sep 17 00:00:00 2001 From: "snakedeploy-bot[bot]" <115615832+snakedeploy-bot[bot]@users.noreply.github.com> Date: Fri, 9 Aug 2024 03:17:12 +0000 Subject: [PATCH 30/62] perf: autobump bio/gatk3/indelrealigner (#3106) Automatic bump of bio/gatk3/indelrealigner. --------- Co-authored-by: snakedeploy-bot[bot] <115615832+snakedeploy-bot[bot]@users.noreply.github.com> --- .../environment.linux-64.pin.txt | 125 +++++++++--------- bio/gatk3/indelrealigner/environment.yaml | 2 +- 2 files changed, 64 insertions(+), 63 deletions(-) diff --git a/bio/gatk3/indelrealigner/environment.linux-64.pin.txt b/bio/gatk3/indelrealigner/environment.linux-64.pin.txt index 12c81bf584f..94dfb406cb0 100644 --- a/bio/gatk3/indelrealigner/environment.linux-64.pin.txt +++ b/bio/gatk3/indelrealigner/environment.linux-64.pin.txt @@ -4,26 +4,27 @@ @EXPLICIT https://conda.anaconda.org/conda-forge/linux-64/_libgcc_mutex-0.1-conda_forge.tar.bz2#d7c89558ba9fa0495403155b64376d81 https://conda.anaconda.org/conda-forge/noarch/_r-mutex-1.0.1-anacondar_1.tar.bz2#19f9db5f4f1b7f5ef5f6d67207f25f38 +https://conda.anaconda.org/conda-forge/noarch/_sysroot_linux-64_curr_repodata_hack-3-h69a702a_16.conda#1c005af0c6ff22814b7c52ee448d4bea https://conda.anaconda.org/conda-forge/linux-64/ca-certificates-2024.7.4-hbcca054_0.conda#23ab7665c5f63cfb9f1f6195256daac6 https://conda.anaconda.org/conda-forge/noarch/font-ttf-dejavu-sans-mono-2.37-hab24e00_0.tar.bz2#0c96522c6bdaed4b1566d11387caaf45 https://conda.anaconda.org/conda-forge/noarch/font-ttf-inconsolata-3.000-h77eed37_0.tar.bz2#34893075a5c9e55cdafac56607368fc6 https://conda.anaconda.org/conda-forge/noarch/font-ttf-source-code-pro-2.038-h77eed37_0.tar.bz2#4d59c254e01d9cde7957100457e2d5fb https://conda.anaconda.org/conda-forge/noarch/font-ttf-ubuntu-0.83-h77eed37_2.conda#cbbe59391138ea5ad3658c76912e147f -https://conda.anaconda.org/conda-forge/noarch/kernel-headers_linux-64-2.6.32-he073ed8_17.conda#d731b543793afc0433c4fd593e693fce https://conda.anaconda.org/conda-forge/linux-64/ld_impl_linux-64-2.40-hf3520f5_7.conda#b80f2f396ca2c28b8c14c437a4ed1e74 https://conda.anaconda.org/conda-forge/noarch/libgcc-devel_linux-64-14.1.0-h5d3d1c9_100.conda#6d4f65dc440f7b3422113b135be19703 https://conda.anaconda.org/conda-forge/noarch/libstdcxx-devel_linux-64-14.1.0-h5d3d1c9_100.conda#cedc62fd8c4cf28f23d3cd5db7839e99 -https://conda.anaconda.org/conda-forge/linux-64/openjdk-8.0.412-hd590300_0.conda#7628220319162f8a7b27f8938a0fc484 +https://conda.anaconda.org/conda-forge/linux-64/openjdk-8.0.412-hd590300_1.conda#d2a3445233d7c7b1c739eb088c6703cf https://conda.anaconda.org/conda-forge/noarch/tzdata-2024a-h0c530f3_0.conda#161081fc7cec0bfda0d86d7cb595f8d8 https://conda.anaconda.org/conda-forge/noarch/fonts-conda-forge-1-0.tar.bz2#f766549260d6815b0c52253f1fb1bb29 +https://conda.anaconda.org/conda-forge/noarch/kernel-headers_linux-64-3.10.0-h4a8ded7_16.conda#ff7f38675b226cfb855aebfc32a13e31 https://conda.anaconda.org/conda-forge/linux-64/libgomp-14.1.0-h77fa898_0.conda#ae061a5ed5f05818acdf9adab72c146d -https://conda.anaconda.org/conda-forge/noarch/sysroot_linux-64-2.12-he073ed8_17.conda#595db67e32b276298ff3d94d07d47fbf https://conda.anaconda.org/conda-forge/linux-64/_openmp_mutex-4.5-2_gnu.tar.bz2#73aaf86a425cc6e73fcf236a5a46396d -https://conda.anaconda.org/conda-forge/linux-64/binutils_impl_linux-64-2.40-ha1999f0_7.conda#3f840c7ed70a96b5ebde8044b2f36f32 https://conda.anaconda.org/conda-forge/noarch/fonts-conda-ecosystem-1-0.tar.bz2#fee5683a3f04bd15cbd8318b096a27ab +https://conda.anaconda.org/conda-forge/noarch/sysroot_linux-64-2.17-h4a8ded7_16.conda#223fe8a3ff6d5e78484a9d58eb34d055 +https://conda.anaconda.org/conda-forge/linux-64/binutils_impl_linux-64-2.40-ha1999f0_7.conda#3f840c7ed70a96b5ebde8044b2f36f32 https://conda.anaconda.org/conda-forge/linux-64/libgcc-ng-14.1.0-h77fa898_0.conda#ca0fad6a41ddaef54a153b78eccb5037 -https://conda.anaconda.org/conda-forge/linux-64/bzip2-1.0.8-hd590300_5.conda#69b8b6202a07720f448be700e300ccf4 -https://conda.anaconda.org/conda-forge/linux-64/c-ares-1.28.1-hd590300_0.conda#dcde58ff9a1f30b0037a2315d1846d1f +https://conda.anaconda.org/conda-forge/linux-64/bzip2-1.0.8-h4bc722e_7.conda#62ee74e96c5ebb0af99386de58cf9553 +https://conda.anaconda.org/conda-forge/linux-64/c-ares-1.32.3-h4bc722e_0.conda#7624e34ee6baebfc80d67bac76cc9d9d https://conda.anaconda.org/conda-forge/linux-64/fribidi-1.0.10-h36c2ea0_0.tar.bz2#ac7bc6a654f8f41b352b38f4051135f8 https://conda.anaconda.org/conda-forge/linux-64/keyutils-1.6.1-h166bdaf_0.tar.bz2#30186d27e2c9fa62b45fb1476b7200e3 https://conda.anaconda.org/conda-forge/linux-64/libdeflate-1.20-hd590300_0.conda#8e88f9389f1165d7c0936fe40d9a9a79 @@ -41,7 +42,7 @@ https://conda.anaconda.org/conda-forge/linux-64/libxcrypt-4.4.36-hd590300_1.cond https://conda.anaconda.org/conda-forge/linux-64/libzlib-1.3.1-h4ab18f5_1.conda#57d7dc60e9325e3de37ff8dffd18e814 https://conda.anaconda.org/conda-forge/linux-64/make-4.3-hd18ef5c_1.tar.bz2#4049ebfd3190b580dffe76daed26155a https://conda.anaconda.org/conda-forge/linux-64/ncurses-6.5-h59595ed_0.conda#fcea371545eda051b6deafb24889fc69 -https://conda.anaconda.org/conda-forge/linux-64/openssl-3.3.1-h4ab18f5_1.conda#b1e9d076f14e8d776213fd5047b4c3d9 +https://conda.anaconda.org/conda-forge/linux-64/openssl-3.3.1-h4bc722e_2.conda#e1b454497f9f7c1147fdde4b53f1b512 https://conda.anaconda.org/conda-forge/linux-64/pthread-stubs-0.4-h36c2ea0_1001.tar.bz2#22dad4df6e8630e8dff2428f6f6a7036 https://conda.anaconda.org/conda-forge/linux-64/sed-4.8-he412f7d_0.tar.bz2#7362f0042e95681f5d371c46c83ebd08 https://conda.anaconda.org/conda-forge/linux-64/xorg-kbproto-1.0.7-h7f98852_1002.tar.bz2#4b230e8381279d76131116660f5a241a @@ -54,7 +55,7 @@ https://conda.anaconda.org/conda-forge/linux-64/xorg-xproto-7.0.31-h7f98852_1007 https://conda.anaconda.org/conda-forge/linux-64/xz-5.2.6-h166bdaf_0.tar.bz2#2161070d867d1b1204ea749c8eec4ef0 https://conda.anaconda.org/conda-forge/linux-64/expat-2.6.2-h59595ed_0.conda#53fb86322bdb89496d7579fe3f02fd61 https://conda.anaconda.org/conda-forge/linux-64/graphite2-1.3.13-h59595ed_1003.conda#f87c7b7c2cb45f323ffbce941c78ab7c -https://conda.anaconda.org/conda-forge/linux-64/icu-73.2-h59595ed_0.conda#cc47e1facc155f91abd89b11e48e72ff +https://conda.anaconda.org/conda-forge/linux-64/icu-75.1-he02047a_0.conda#8b189310083baabfb622af68fd9d3ae3 https://conda.anaconda.org/conda-forge/linux-64/lerc-4.0.0-h27087fc_0.tar.bz2#76bbff344f0134279f225174e9064c8f https://conda.anaconda.org/conda-forge/linux-64/libedit-3.1.20191231-he28a2e2_2.tar.bz2#4d331e44109e3f0e19b4cb8f9b82f3e1 https://conda.anaconda.org/conda-forge/linux-64/libgfortran-ng-14.1.0-h69a702a_0.conda#f4ca84fbd6d06b0a052fb2d5b96dde41 @@ -75,69 +76,69 @@ https://conda.anaconda.org/conda-forge/linux-64/bwidget-1.9.14-ha770c72_1.tar.bz https://conda.anaconda.org/conda-forge/linux-64/freetype-2.12.1-h267a509_2.conda#9ae35c3d96db2c94ce0cef86efdfa2cb https://conda.anaconda.org/conda-forge/linux-64/gcc_impl_linux-64-14.1.0-h3c94d91_0.conda#b0dd0de49e0f3e34f3f636e5c7d149fe https://conda.anaconda.org/conda-forge/linux-64/krb5-1.21.3-h659f571_0.conda#3f43953b7d3fb3aaa1d0d0723d91e368 -https://conda.anaconda.org/conda-forge/linux-64/libglib-2.80.2-h8a4344b_1.conda#9c406bb3d4dac2b358873e6462496d09 -https://conda.anaconda.org/conda-forge/linux-64/libopenblas-0.3.27-pthreads_h413a1c8_0.conda#a356024784da6dfd4683dc5ecf45b155 +https://conda.anaconda.org/conda-forge/linux-64/libglib-2.80.3-h8a4344b_1.conda#6ea440297aacee4893f02ad759e6ffbc +https://conda.anaconda.org/conda-forge/linux-64/libopenblas-0.3.27-pthreads_hac2b453_1.conda#ae05ece66d3924ac3d48b4aa3fa96cec https://conda.anaconda.org/conda-forge/linux-64/libtiff-4.6.0-h1dd3fc0_3.conda#66f03896ffbe1a110ffda05c7a856504 -https://conda.anaconda.org/conda-forge/linux-64/python-3.12.4-h194c7f8_0_cpython.conda#d73490214f536cccb5819e9873048c92 +https://conda.anaconda.org/conda-forge/linux-64/python-3.12.5-h2ad013b_0_cpython.conda#9c56c4df45f6571b13111d8df2448692 https://conda.anaconda.org/conda-forge/linux-64/tktable-2.10-h8bc8fbc_6.conda#dff3627fec2c0584ded391205295abf0 https://conda.anaconda.org/conda-forge/linux-64/xorg-libx11-1.8.9-hb711507_1.conda#4a6d410296d7e39f00bacdee7df046e9 https://conda.anaconda.org/conda-forge/linux-64/fontconfig-2.14.2-h14ed4e7_0.conda#0f69b688f52ff6da70bccb7ff7001d1d https://conda.anaconda.org/conda-forge/linux-64/gfortran_impl_linux-64-14.1.0-he4a1faa_0.conda#a9ce7cd0848a93a8df88c1fc0ac84d9d -https://conda.anaconda.org/conda-forge/linux-64/gxx_impl_linux-64-14.1.0-h2879b86_0.conda#47d6de998d7a285b98b60bce2fecb54b 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-https://conda.anaconda.org/conda-forge/noarch/r-pillar-1.9.0-r43hc72bb7e_1.conda#7cff01456566a69381d3907d520c10b2 -https://conda.anaconda.org/conda-forge/linux-64/r-tibble-3.2.1-r43h57805ef_2.conda#afa7d3f21fbc5a2fbaa48cb9bacb7bce -https://conda.anaconda.org/conda-forge/noarch/r-ggplot2-3.5.1-r43hc72bb7e_0.conda#efb6b27dba202d74e5f182faae28794a +https://conda.anaconda.org/conda-forge/linux-64/r-base-4.4.1-h745b8e0_14.conda#fb6648c142f3bc891f2bdfd8f2d28340 +https://conda.anaconda.org/conda-forge/linux-64/r-bitops-1.0_8-r44hdb488b9_0.conda#61ca33f2e0ba7d494ea65a526839e418 +https://conda.anaconda.org/conda-forge/linux-64/r-cli-3.6.3-r44h0d4f4ea_1.conda#4f07a3d62def16d73303c8435e17a62e +https://conda.anaconda.org/conda-forge/linux-64/r-colorspace-2.1_1-r44hdb488b9_0.conda#fcc0b0959eb8b3ea4ce2bb8818cea10e +https://conda.anaconda.org/conda-forge/noarch/r-crayon-1.5.3-r44hc72bb7e_1.conda#89626d77a94256b8304bb8fc33d3364c +https://conda.anaconda.org/conda-forge/linux-64/r-fansi-1.0.6-r44hb1dbf0f_1.conda#c4c0d4b82b54899c61c6f3e09b1bcc5c +https://conda.anaconda.org/conda-forge/linux-64/r-farver-2.1.2-r44ha18555a_1.conda#c2cf909117c44802caf096dd8ba8038e +https://conda.anaconda.org/conda-forge/linux-64/r-glue-1.7.0-r44hb1dbf0f_1.conda#353c728f5a70cb0c530c01c47cc6bb66 +https://conda.anaconda.org/conda-forge/noarch/r-gsalib-2.2.1-r44hc72bb7e_3.conda#4c13b89540896e44cee48069cf2ff704 +https://conda.anaconda.org/conda-forge/linux-64/r-gtools-3.9.5-r44hb1dbf0f_1.conda#40f5e42c4673ad0187907d821f44c7e5 +https://conda.anaconda.org/conda-forge/linux-64/r-isoband-0.2.7-r44ha18555a_3.conda#4745fadbe3c521e46d9c9b39148ac3c7 +https://conda.anaconda.org/conda-forge/linux-64/r-kernsmooth-2.23_24-r44hc2011d3_1.conda#fa86b7628e4b5f609bd40cce8a7ae801 +https://conda.anaconda.org/conda-forge/noarch/r-labeling-0.4.3-r44hc72bb7e_1.conda#49f2c043dfb8f5003dea36ae39ca1103 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+https://conda.anaconda.org/conda-forge/linux-64/r-utf8-1.2.4-r44hb1dbf0f_1.conda#11331e679a538de7c85ced8d293394a2 +https://conda.anaconda.org/conda-forge/noarch/r-viridislite-0.4.2-r44hc72bb7e_2.conda#7cf7a6974364e6853f1a06554dfaa3e5 +https://conda.anaconda.org/conda-forge/noarch/r-withr-3.0.1-r44hc72bb7e_0.conda#b9171dfd69c9d0e35ffc8927f79e447f +https://conda.anaconda.org/conda-forge/linux-64/r-catools-1.18.2-r44ha18555a_3.conda#82ce8ed9e8dc9a2f818d89fcf27d4e8f +https://conda.anaconda.org/conda-forge/linux-64/r-ellipsis-0.3.2-r44hb1dbf0f_3.conda#a96cb6b4b61efd45ffe47019af5eb879 +https://conda.anaconda.org/conda-forge/noarch/r-lifecycle-1.0.4-r44hc72bb7e_1.conda#66d0ba7c05d0abfa11d126ba8e2907aa +https://conda.anaconda.org/conda-forge/linux-64/r-matrix-1.6_5-r44he966344_1.conda#bbcb8fe02b64b3b69bf078f2020f7446 +https://conda.anaconda.org/conda-forge/noarch/r-munsell-0.5.1-r44hc72bb7e_1.conda#871dfde2639a8fdfe210eea7c59fd1e8 +https://conda.anaconda.org/conda-forge/linux-64/r-nlme-3.1_165-r44hbcb9c34_1.conda#b579f3ffba329dd5b46bddb429a8aa2e +https://conda.anaconda.org/conda-forge/linux-64/r-plyr-1.8.9-r44ha18555a_1.conda#4d48c0a215274a331bde69cc65a932d2 +https://conda.anaconda.org/conda-forge/noarch/r-gplots-3.1.3.1-r44hc72bb7e_1.conda#d662367291002b1e449f36ef26980cb4 +https://conda.anaconda.org/conda-forge/noarch/r-gtable-0.3.5-r44hc72bb7e_1.conda#c3040db0b657a19a071ed472d24a204d +https://conda.anaconda.org/conda-forge/linux-64/r-mgcv-1.9_1-r44h0d28552_1.conda#3bd992bc484600de3b23809fb76eb7bb +https://conda.anaconda.org/conda-forge/linux-64/r-reshape-0.8.9-r44hc72bb7e_3.conda#76e52127f959b28ff3c41b0493f88b38 +https://conda.anaconda.org/conda-forge/noarch/r-scales-1.3.0-r44hc72bb7e_1.conda#31cda9180dde0613a04a020771eb2d09 +https://conda.anaconda.org/conda-forge/linux-64/r-vctrs-0.6.5-r44h0d4f4ea_1.conda#399bc7872bdb40b5531d887858253e76 +https://conda.anaconda.org/conda-forge/noarch/r-pillar-1.9.0-r44hc72bb7e_2.conda#3ec6418c9af0a90d4513cadfe0ef863a +https://conda.anaconda.org/conda-forge/linux-64/r-tibble-3.2.1-r44hdb488b9_3.conda#03203ac70558ba5bb836d1cb641f1b87 +https://conda.anaconda.org/conda-forge/noarch/r-ggplot2-3.5.1-r44hc72bb7e_1.conda#c6209f7de229696ebd0086e7c27a02ac https://conda.anaconda.org/bioconda/noarch/gatk-3.8-hdfd78af_12.tar.bz2#ce94fe85517155af78e62d1412785d7e diff --git a/bio/gatk3/indelrealigner/environment.yaml b/bio/gatk3/indelrealigner/environment.yaml index eaa654dc24a..cfa44daec8d 100644 --- a/bio/gatk3/indelrealigner/environment.yaml +++ b/bio/gatk3/indelrealigner/environment.yaml @@ -4,5 +4,5 @@ channels: - nodefaults dependencies: - gatk =3.8 - - python =3.12.4 + - python =3.12.5 - snakemake-wrapper-utils =0.6.2 From b1c333462d4540a4ed995af2a190bdab0f43e66a Mon Sep 17 00:00:00 2001 From: "snakedeploy-bot[bot]" <115615832+snakedeploy-bot[bot]@users.noreply.github.com> Date: Fri, 9 Aug 2024 03:42:32 +0000 Subject: [PATCH 31/62] perf: autobump bio/last/lastdb (#3107) Automatic bump of bio/last/lastdb. --------- Co-authored-by: snakedeploy-bot[bot] <115615832+snakedeploy-bot[bot]@users.noreply.github.com> --- bio/last/lastdb/environment.linux-64.pin.txt | 30 ++++++++++---------- bio/last/lastdb/environment.yaml | 2 +- 2 files changed, 16 insertions(+), 16 deletions(-) diff --git a/bio/last/lastdb/environment.linux-64.pin.txt b/bio/last/lastdb/environment.linux-64.pin.txt index b6d31021380..fb563b49100 100644 --- a/bio/last/lastdb/environment.linux-64.pin.txt +++ b/bio/last/lastdb/environment.linux-64.pin.txt @@ -3,26 +3,26 @@ # platform: linux-64 @EXPLICIT https://conda.anaconda.org/conda-forge/linux-64/_libgcc_mutex-0.1-conda_forge.tar.bz2#d7c89558ba9fa0495403155b64376d81 -https://conda.anaconda.org/conda-forge/linux-64/ca-certificates-2024.6.2-hbcca054_0.conda#847c3c2905cc467cea52c24f9cfa8080 +https://conda.anaconda.org/conda-forge/linux-64/ca-certificates-2024.7.4-hbcca054_0.conda#23ab7665c5f63cfb9f1f6195256daac6 https://conda.anaconda.org/conda-forge/linux-64/ld_impl_linux-64-2.40-hf3520f5_7.conda#b80f2f396ca2c28b8c14c437a4ed1e74 https://conda.anaconda.org/conda-forge/linux-64/python_abi-3.12-4_cp312.conda#dccc2d142812964fcc6abdc97b672dff https://conda.anaconda.org/conda-forge/noarch/tzdata-2024a-h0c530f3_0.conda#161081fc7cec0bfda0d86d7cb595f8d8 -https://conda.anaconda.org/conda-forge/linux-64/libgomp-13.2.0-h77fa898_11.conda#8c462ced2af33648195dc9459f331f31 +https://conda.anaconda.org/conda-forge/linux-64/libgomp-14.1.0-h77fa898_0.conda#ae061a5ed5f05818acdf9adab72c146d https://conda.anaconda.org/conda-forge/linux-64/_openmp_mutex-4.5-2_gnu.tar.bz2#73aaf86a425cc6e73fcf236a5a46396d -https://conda.anaconda.org/conda-forge/linux-64/libgcc-ng-13.2.0-h77fa898_11.conda#0b3b218a596bb4c3854cc9ee799f94e5 -https://conda.anaconda.org/conda-forge/linux-64/bzip2-1.0.8-hd590300_5.conda#69b8b6202a07720f448be700e300ccf4 -https://conda.anaconda.org/conda-forge/linux-64/libdeflate-1.20-hd590300_0.conda#8e88f9389f1165d7c0936fe40d9a9a79 +https://conda.anaconda.org/conda-forge/linux-64/libgcc-ng-14.1.0-h77fa898_0.conda#ca0fad6a41ddaef54a153b78eccb5037 +https://conda.anaconda.org/conda-forge/linux-64/bzip2-1.0.8-h4bc722e_7.conda#62ee74e96c5ebb0af99386de58cf9553 +https://conda.anaconda.org/conda-forge/linux-64/libdeflate-1.21-h4bc722e_0.conda#36ce76665bf67f5aac36be7a0d21b7f3 https://conda.anaconda.org/conda-forge/linux-64/libexpat-2.6.2-h59595ed_0.conda#e7ba12deb7020dd080c6c70e7b6f6a3d https://conda.anaconda.org/conda-forge/linux-64/libffi-3.4.2-h7f98852_5.tar.bz2#d645c6d2ac96843a2bfaccd2d62b3ac3 https://conda.anaconda.org/conda-forge/linux-64/libjpeg-turbo-3.0.0-hd590300_1.conda#ea25936bb4080d843790b586850f82b8 https://conda.anaconda.org/conda-forge/linux-64/libnsl-2.0.1-hd590300_0.conda#30fd6e37fe21f86f4bd26d6ee73eeec7 -https://conda.anaconda.org/conda-forge/linux-64/libstdcxx-ng-13.2.0-hc0a3c3a_11.conda#eaa8ea74083fb4a78ae19e431e556003 +https://conda.anaconda.org/conda-forge/linux-64/libstdcxx-ng-14.1.0-hc0a3c3a_0.conda#1cb187a157136398ddbaae90713e2498 https://conda.anaconda.org/conda-forge/linux-64/libuuid-2.38.1-h0b41bf4_0.conda#40b61aab5c7ba9ff276c41cfffe6b80b https://conda.anaconda.org/conda-forge/linux-64/libwebp-base-1.4.0-hd590300_0.conda#b26e8aa824079e1be0294e7152ca4559 https://conda.anaconda.org/conda-forge/linux-64/libxcrypt-4.4.36-hd590300_1.conda#5aa797f8787fe7a17d1b0821485b5adc https://conda.anaconda.org/conda-forge/linux-64/libzlib-1.3.1-h4ab18f5_1.conda#57d7dc60e9325e3de37ff8dffd18e814 https://conda.anaconda.org/conda-forge/linux-64/ncurses-6.5-h59595ed_0.conda#fcea371545eda051b6deafb24889fc69 -https://conda.anaconda.org/conda-forge/linux-64/openssl-3.3.1-h4ab18f5_0.conda#a41fa0e391cc9e0d6b78ac69ca047a6c +https://conda.anaconda.org/conda-forge/linux-64/openssl-3.3.1-h4bc722e_2.conda#e1b454497f9f7c1147fdde4b53f1b512 https://conda.anaconda.org/conda-forge/linux-64/pthread-stubs-0.4-h36c2ea0_1001.tar.bz2#22dad4df6e8630e8dff2428f6f6a7036 https://conda.anaconda.org/conda-forge/linux-64/xorg-libxau-1.0.11-hd590300_0.conda#2c80dc38fface310c9bd81b17037fee5 https://conda.anaconda.org/conda-forge/linux-64/xorg-libxdmcp-1.1.3-h7f98852_0.tar.bz2#be93aabceefa2fac576e971aef407908 @@ -37,13 +37,13 @@ https://conda.anaconda.org/conda-forge/linux-64/tk-8.6.13-noxft_h4845f30_101.con https://conda.anaconda.org/conda-forge/linux-64/zlib-1.3.1-h4ab18f5_1.conda#9653f1bf3766164d0e65fa723cabbc54 https://conda.anaconda.org/conda-forge/linux-64/zstd-1.5.6-ha6fb4c9_0.conda#4d056880988120e29d75bfff282e0f45 https://conda.anaconda.org/conda-forge/linux-64/freetype-2.12.1-h267a509_2.conda#9ae35c3d96db2c94ce0cef86efdfa2cb -https://conda.anaconda.org/conda-forge/linux-64/libtiff-4.6.0-h1dd3fc0_3.conda#66f03896ffbe1a110ffda05c7a856504 -https://conda.anaconda.org/conda-forge/linux-64/parallel-20240522-ha770c72_0.conda#95444bc23d494d0b06405bea54c7cd1f -https://conda.anaconda.org/conda-forge/linux-64/python-3.12.4-h194c7f8_0_cpython.conda#d73490214f536cccb5819e9873048c92 +https://conda.anaconda.org/conda-forge/linux-64/libtiff-4.6.0-h46a8edc_4.conda#a7e3a62981350e232e0e7345b5aea580 +https://conda.anaconda.org/conda-forge/linux-64/parallel-20240722-ha770c72_0.conda#acad361a391f190dc2fa629a2814fdcf +https://conda.anaconda.org/conda-forge/linux-64/python-3.12.5-h2ad013b_0_cpython.conda#9c56c4df45f6571b13111d8df2448692 https://conda.anaconda.org/conda-forge/linux-64/lcms2-2.16-hb7c19ff_0.conda#51bb7010fc86f70eee639b4bb7a894f5 https://conda.anaconda.org/conda-forge/linux-64/openjpeg-2.5.2-h488ebb8_0.conda#7f2e286780f072ed750df46dc2631138 -https://conda.anaconda.org/conda-forge/noarch/setuptools-70.1.0-pyhd8ed1ab_0.conda#258e66f95f814d51ada2a1fe9274039b -https://conda.anaconda.org/conda-forge/noarch/wheel-0.43.0-pyhd8ed1ab_1.conda#0b5293a157c2b5cd513dd1b03d8d3aae -https://conda.anaconda.org/conda-forge/linux-64/pillow-10.3.0-py312h287a98d_1.conda#b1325cda3f250f9f842180607054e6ed -https://conda.anaconda.org/conda-forge/noarch/pip-24.0-pyhd8ed1ab_0.conda#f586ac1e56c8638b64f9c8122a7b8a67 -https://conda.anaconda.org/bioconda/linux-64/last-1548-h43eeafb_0.tar.bz2#53a012d273077c23ff3d4d43b687b2d5 +https://conda.anaconda.org/conda-forge/noarch/setuptools-72.1.0-pyhd8ed1ab_0.conda#e06d4c26df4f958a8d38696f2c344d15 +https://conda.anaconda.org/conda-forge/noarch/wheel-0.44.0-pyhd8ed1ab_0.conda#d44e3b085abcaef02983c6305b84b584 +https://conda.anaconda.org/conda-forge/linux-64/pillow-10.4.0-py312h287a98d_0.conda#59ea71eed98aee0bebbbdd3b118167c7 +https://conda.anaconda.org/conda-forge/noarch/pip-24.2-pyhd8ed1ab_0.conda#6721aef6bfe5937abe70181545dd2c51 +https://conda.anaconda.org/bioconda/linux-64/last-1550-h43eeafb_0.tar.bz2#ee6566f27bbf9c35413359a8007d37ff diff --git a/bio/last/lastdb/environment.yaml b/bio/last/lastdb/environment.yaml index a310d945e81..3cd69035c86 100644 --- a/bio/last/lastdb/environment.yaml +++ b/bio/last/lastdb/environment.yaml @@ -3,4 +3,4 @@ channels: - bioconda - nodefaults dependencies: - - last =1548 + - last =1550 From 9f7a264c5ceb560008945a4520960e219f470827 Mon Sep 17 00:00:00 2001 From: "snakedeploy-bot[bot]" <115615832+snakedeploy-bot[bot]@users.noreply.github.com> Date: Fri, 9 Aug 2024 03:43:35 +0000 Subject: [PATCH 32/62] perf: autobump bio/last/lastal (#3108) Automatic bump of bio/last/lastal. --------- Co-authored-by: snakedeploy-bot[bot] <115615832+snakedeploy-bot[bot]@users.noreply.github.com> --- bio/last/lastal/environment.linux-64.pin.txt | 30 ++++++++++---------- bio/last/lastal/environment.yaml | 2 +- 2 files changed, 16 insertions(+), 16 deletions(-) diff --git a/bio/last/lastal/environment.linux-64.pin.txt b/bio/last/lastal/environment.linux-64.pin.txt index b6d31021380..fb563b49100 100644 --- a/bio/last/lastal/environment.linux-64.pin.txt +++ b/bio/last/lastal/environment.linux-64.pin.txt @@ -3,26 +3,26 @@ # platform: linux-64 @EXPLICIT https://conda.anaconda.org/conda-forge/linux-64/_libgcc_mutex-0.1-conda_forge.tar.bz2#d7c89558ba9fa0495403155b64376d81 -https://conda.anaconda.org/conda-forge/linux-64/ca-certificates-2024.6.2-hbcca054_0.conda#847c3c2905cc467cea52c24f9cfa8080 +https://conda.anaconda.org/conda-forge/linux-64/ca-certificates-2024.7.4-hbcca054_0.conda#23ab7665c5f63cfb9f1f6195256daac6 https://conda.anaconda.org/conda-forge/linux-64/ld_impl_linux-64-2.40-hf3520f5_7.conda#b80f2f396ca2c28b8c14c437a4ed1e74 https://conda.anaconda.org/conda-forge/linux-64/python_abi-3.12-4_cp312.conda#dccc2d142812964fcc6abdc97b672dff https://conda.anaconda.org/conda-forge/noarch/tzdata-2024a-h0c530f3_0.conda#161081fc7cec0bfda0d86d7cb595f8d8 -https://conda.anaconda.org/conda-forge/linux-64/libgomp-13.2.0-h77fa898_11.conda#8c462ced2af33648195dc9459f331f31 +https://conda.anaconda.org/conda-forge/linux-64/libgomp-14.1.0-h77fa898_0.conda#ae061a5ed5f05818acdf9adab72c146d https://conda.anaconda.org/conda-forge/linux-64/_openmp_mutex-4.5-2_gnu.tar.bz2#73aaf86a425cc6e73fcf236a5a46396d -https://conda.anaconda.org/conda-forge/linux-64/libgcc-ng-13.2.0-h77fa898_11.conda#0b3b218a596bb4c3854cc9ee799f94e5 -https://conda.anaconda.org/conda-forge/linux-64/bzip2-1.0.8-hd590300_5.conda#69b8b6202a07720f448be700e300ccf4 -https://conda.anaconda.org/conda-forge/linux-64/libdeflate-1.20-hd590300_0.conda#8e88f9389f1165d7c0936fe40d9a9a79 +https://conda.anaconda.org/conda-forge/linux-64/libgcc-ng-14.1.0-h77fa898_0.conda#ca0fad6a41ddaef54a153b78eccb5037 +https://conda.anaconda.org/conda-forge/linux-64/bzip2-1.0.8-h4bc722e_7.conda#62ee74e96c5ebb0af99386de58cf9553 +https://conda.anaconda.org/conda-forge/linux-64/libdeflate-1.21-h4bc722e_0.conda#36ce76665bf67f5aac36be7a0d21b7f3 https://conda.anaconda.org/conda-forge/linux-64/libexpat-2.6.2-h59595ed_0.conda#e7ba12deb7020dd080c6c70e7b6f6a3d https://conda.anaconda.org/conda-forge/linux-64/libffi-3.4.2-h7f98852_5.tar.bz2#d645c6d2ac96843a2bfaccd2d62b3ac3 https://conda.anaconda.org/conda-forge/linux-64/libjpeg-turbo-3.0.0-hd590300_1.conda#ea25936bb4080d843790b586850f82b8 https://conda.anaconda.org/conda-forge/linux-64/libnsl-2.0.1-hd590300_0.conda#30fd6e37fe21f86f4bd26d6ee73eeec7 -https://conda.anaconda.org/conda-forge/linux-64/libstdcxx-ng-13.2.0-hc0a3c3a_11.conda#eaa8ea74083fb4a78ae19e431e556003 +https://conda.anaconda.org/conda-forge/linux-64/libstdcxx-ng-14.1.0-hc0a3c3a_0.conda#1cb187a157136398ddbaae90713e2498 https://conda.anaconda.org/conda-forge/linux-64/libuuid-2.38.1-h0b41bf4_0.conda#40b61aab5c7ba9ff276c41cfffe6b80b https://conda.anaconda.org/conda-forge/linux-64/libwebp-base-1.4.0-hd590300_0.conda#b26e8aa824079e1be0294e7152ca4559 https://conda.anaconda.org/conda-forge/linux-64/libxcrypt-4.4.36-hd590300_1.conda#5aa797f8787fe7a17d1b0821485b5adc https://conda.anaconda.org/conda-forge/linux-64/libzlib-1.3.1-h4ab18f5_1.conda#57d7dc60e9325e3de37ff8dffd18e814 https://conda.anaconda.org/conda-forge/linux-64/ncurses-6.5-h59595ed_0.conda#fcea371545eda051b6deafb24889fc69 -https://conda.anaconda.org/conda-forge/linux-64/openssl-3.3.1-h4ab18f5_0.conda#a41fa0e391cc9e0d6b78ac69ca047a6c +https://conda.anaconda.org/conda-forge/linux-64/openssl-3.3.1-h4bc722e_2.conda#e1b454497f9f7c1147fdde4b53f1b512 https://conda.anaconda.org/conda-forge/linux-64/pthread-stubs-0.4-h36c2ea0_1001.tar.bz2#22dad4df6e8630e8dff2428f6f6a7036 https://conda.anaconda.org/conda-forge/linux-64/xorg-libxau-1.0.11-hd590300_0.conda#2c80dc38fface310c9bd81b17037fee5 https://conda.anaconda.org/conda-forge/linux-64/xorg-libxdmcp-1.1.3-h7f98852_0.tar.bz2#be93aabceefa2fac576e971aef407908 @@ -37,13 +37,13 @@ https://conda.anaconda.org/conda-forge/linux-64/tk-8.6.13-noxft_h4845f30_101.con https://conda.anaconda.org/conda-forge/linux-64/zlib-1.3.1-h4ab18f5_1.conda#9653f1bf3766164d0e65fa723cabbc54 https://conda.anaconda.org/conda-forge/linux-64/zstd-1.5.6-ha6fb4c9_0.conda#4d056880988120e29d75bfff282e0f45 https://conda.anaconda.org/conda-forge/linux-64/freetype-2.12.1-h267a509_2.conda#9ae35c3d96db2c94ce0cef86efdfa2cb -https://conda.anaconda.org/conda-forge/linux-64/libtiff-4.6.0-h1dd3fc0_3.conda#66f03896ffbe1a110ffda05c7a856504 -https://conda.anaconda.org/conda-forge/linux-64/parallel-20240522-ha770c72_0.conda#95444bc23d494d0b06405bea54c7cd1f -https://conda.anaconda.org/conda-forge/linux-64/python-3.12.4-h194c7f8_0_cpython.conda#d73490214f536cccb5819e9873048c92 +https://conda.anaconda.org/conda-forge/linux-64/libtiff-4.6.0-h46a8edc_4.conda#a7e3a62981350e232e0e7345b5aea580 +https://conda.anaconda.org/conda-forge/linux-64/parallel-20240722-ha770c72_0.conda#acad361a391f190dc2fa629a2814fdcf +https://conda.anaconda.org/conda-forge/linux-64/python-3.12.5-h2ad013b_0_cpython.conda#9c56c4df45f6571b13111d8df2448692 https://conda.anaconda.org/conda-forge/linux-64/lcms2-2.16-hb7c19ff_0.conda#51bb7010fc86f70eee639b4bb7a894f5 https://conda.anaconda.org/conda-forge/linux-64/openjpeg-2.5.2-h488ebb8_0.conda#7f2e286780f072ed750df46dc2631138 -https://conda.anaconda.org/conda-forge/noarch/setuptools-70.1.0-pyhd8ed1ab_0.conda#258e66f95f814d51ada2a1fe9274039b -https://conda.anaconda.org/conda-forge/noarch/wheel-0.43.0-pyhd8ed1ab_1.conda#0b5293a157c2b5cd513dd1b03d8d3aae -https://conda.anaconda.org/conda-forge/linux-64/pillow-10.3.0-py312h287a98d_1.conda#b1325cda3f250f9f842180607054e6ed -https://conda.anaconda.org/conda-forge/noarch/pip-24.0-pyhd8ed1ab_0.conda#f586ac1e56c8638b64f9c8122a7b8a67 -https://conda.anaconda.org/bioconda/linux-64/last-1548-h43eeafb_0.tar.bz2#53a012d273077c23ff3d4d43b687b2d5 +https://conda.anaconda.org/conda-forge/noarch/setuptools-72.1.0-pyhd8ed1ab_0.conda#e06d4c26df4f958a8d38696f2c344d15 +https://conda.anaconda.org/conda-forge/noarch/wheel-0.44.0-pyhd8ed1ab_0.conda#d44e3b085abcaef02983c6305b84b584 +https://conda.anaconda.org/conda-forge/linux-64/pillow-10.4.0-py312h287a98d_0.conda#59ea71eed98aee0bebbbdd3b118167c7 +https://conda.anaconda.org/conda-forge/noarch/pip-24.2-pyhd8ed1ab_0.conda#6721aef6bfe5937abe70181545dd2c51 +https://conda.anaconda.org/bioconda/linux-64/last-1550-h43eeafb_0.tar.bz2#ee6566f27bbf9c35413359a8007d37ff diff --git a/bio/last/lastal/environment.yaml b/bio/last/lastal/environment.yaml index a310d945e81..3cd69035c86 100644 --- a/bio/last/lastal/environment.yaml +++ b/bio/last/lastal/environment.yaml @@ -3,4 +3,4 @@ channels: - bioconda - nodefaults dependencies: - - last =1548 + - last =1550 From a870b8ef9bc89a18b093dc6303048b5e1202f740 Mon Sep 17 00:00:00 2001 From: "snakedeploy-bot[bot]" <115615832+snakedeploy-bot[bot]@users.noreply.github.com> Date: Fri, 9 Aug 2024 03:50:37 +0000 Subject: [PATCH 33/62] perf: autobump bio/mapdamage2 (#3109) Automatic bump of bio/mapdamage2. --------- Co-authored-by: snakedeploy-bot[bot] <115615832+snakedeploy-bot[bot]@users.noreply.github.com> --- bio/mapdamage2/environment.linux-64.pin.txt | 153 ++++++++++---------- bio/mapdamage2/environment.yaml | 2 +- 2 files changed, 78 insertions(+), 77 deletions(-) diff --git a/bio/mapdamage2/environment.linux-64.pin.txt b/bio/mapdamage2/environment.linux-64.pin.txt index 2ce098a99ae..ebab1cb425a 100644 --- a/bio/mapdamage2/environment.linux-64.pin.txt +++ b/bio/mapdamage2/environment.linux-64.pin.txt @@ -4,44 +4,45 @@ @EXPLICIT https://conda.anaconda.org/conda-forge/linux-64/_libgcc_mutex-0.1-conda_forge.tar.bz2#d7c89558ba9fa0495403155b64376d81 https://conda.anaconda.org/conda-forge/noarch/_r-mutex-1.0.1-anacondar_1.tar.bz2#19f9db5f4f1b7f5ef5f6d67207f25f38 -https://conda.anaconda.org/conda-forge/linux-64/ca-certificates-2024.6.2-hbcca054_0.conda#847c3c2905cc467cea52c24f9cfa8080 +https://conda.anaconda.org/conda-forge/noarch/_sysroot_linux-64_curr_repodata_hack-3-h69a702a_16.conda#1c005af0c6ff22814b7c52ee448d4bea +https://conda.anaconda.org/conda-forge/linux-64/ca-certificates-2024.7.4-hbcca054_0.conda#23ab7665c5f63cfb9f1f6195256daac6 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+https://conda.anaconda.org/conda-forge/linux-64/harfbuzz-9.0.0-hda332d3_1.conda#76b32dcf243444aea9c6b804bcfa40b8 +https://conda.anaconda.org/conda-forge/linux-64/pango-1.54.0-h4c5309f_1.conda#7df02e445367703cd87a574046e3a6f0 +https://conda.anaconda.org/conda-forge/linux-64/r-base-4.3.3-h9967228_13.conda#d27cdc47236c6dfeface59c344494495 +https://conda.anaconda.org/conda-forge/linux-64/r-cli-3.6.3-r43h0d4f4ea_1.conda#ba1f08e0eab53429d77026adb68960a5 +https://conda.anaconda.org/conda-forge/noarch/r-codetools-0.2_20-r43hc72bb7e_1.conda#f54a935134de901af63096b29a56697e +https://conda.anaconda.org/conda-forge/linux-64/r-colorspace-2.1_1-r43hdb488b9_0.conda#0c6d4c26ca41246a4053d79e1b4d78ff +https://conda.anaconda.org/conda-forge/noarch/r-crayon-1.5.3-r43hc72bb7e_1.conda#bafc77be1942ea00228cf18d2cb30e35 +https://conda.anaconda.org/conda-forge/linux-64/r-fansi-1.0.6-r43hb1dbf0f_1.conda#4c17a0f74a974316fdfafa5a9fe91b52 +https://conda.anaconda.org/conda-forge/linux-64/r-farver-2.1.2-r43ha18555a_1.conda#85a82a5b78397daf57f002120aed9e3e +https://conda.anaconda.org/conda-forge/linux-64/r-glue-1.7.0-r43hb1dbf0f_1.conda#94cbb45d60c60af1fbcf0cf20ad0baa6 +https://conda.anaconda.org/conda-forge/noarch/r-inline-0.3.19-r43hc72bb7e_3.conda#9b365560754adad8bd6710687c3833f9 +https://conda.anaconda.org/conda-forge/linux-64/r-isoband-0.2.7-r43ha18555a_3.conda#39459e8609d9461d90ee0683a7fd2f3a +https://conda.anaconda.org/conda-forge/noarch/r-iterators-1.0.14-r43hc72bb7e_3.conda#982226a9b2f88353204d23b7369683d7 +https://conda.anaconda.org/conda-forge/noarch/r-labeling-0.4.3-r43hc72bb7e_1.conda#0464c37b6ff6701cbb8606e8f4bfebe4 +https://conda.anaconda.org/conda-forge/linux-64/r-lattice-0.22_6-r43hb1dbf0f_1.conda#e42a7ddaeeea0096c4f6df18fb5274e3 +https://conda.anaconda.org/conda-forge/linux-64/r-magrittr-2.0.3-r43hb1dbf0f_3.conda#fc61bcf37e59037b486c8841a704e9da +https://conda.anaconda.org/conda-forge/linux-64/r-mass-7.3_60.0.1-r43hb1dbf0f_1.conda#c3c9184486ccabe19b86aba11351652e +https://conda.anaconda.org/conda-forge/noarch/r-pkgconfig-2.0.3-r43hc72bb7e_4.conda#509adf7f5bc34d77064f28f487d7fa6e +https://conda.anaconda.org/conda-forge/noarch/r-r6-2.5.1-r43hc72bb7e_3.conda#66ea76748b9fac0ca0ef549f796228d3 +https://conda.anaconda.org/conda-forge/noarch/r-rcolorbrewer-1.1_3-r43h785f33e_3.conda#ceb1c167b7d9e5eefed0ecbe759540de +https://conda.anaconda.org/conda-forge/linux-64/r-rcpp-1.0.13-r43h0d4f4ea_0.conda#4bdf774ca022b130631769de75f2e3b7 +https://conda.anaconda.org/conda-forge/linux-64/r-rlang-1.1.4-r43ha18555a_1.conda#e9f6f76e66306bd6483935ad4c79ac28 +https://conda.anaconda.org/conda-forge/linux-64/r-utf8-1.2.4-r43hb1dbf0f_1.conda#6337f1f20dea2a325142d2b7b1b7d42c +https://conda.anaconda.org/conda-forge/noarch/r-viridislite-0.4.2-r43hc72bb7e_2.conda#2a5b8c2803b5714f3319a238c66cc9e7 +https://conda.anaconda.org/conda-forge/noarch/r-withr-3.0.1-r43hc72bb7e_0.conda#7d7e5e3740a49c0fe78ff729d49ea1a5 +https://conda.anaconda.org/conda-forge/linux-64/r-ellipsis-0.3.2-r43hb1dbf0f_3.conda#b8349582a31b17184a7674f4c847a5ad +https://conda.anaconda.org/conda-forge/noarch/r-foreach-1.5.2-r43hc72bb7e_3.conda#1b0d9e2f20eead453cf64c3257076abd +https://conda.anaconda.org/conda-forge/noarch/r-lifecycle-1.0.4-r43hc72bb7e_1.conda#7a0a8ba1fe2cf12b39062d8291e2fca8 +https://conda.anaconda.org/conda-forge/linux-64/r-matrix-1.6_5-r43he966344_1.conda#df8a1175a62460e02dbf340966cbfeab +https://conda.anaconda.org/conda-forge/noarch/r-munsell-0.5.1-r43hc72bb7e_1.conda#8b2f9bb8064ae0896ffedd984661a2d5 +https://conda.anaconda.org/conda-forge/linux-64/r-nlme-3.1_165-r43hbcb9c34_1.conda#ae3f1ce6e352a9089f639044764c533f +https://conda.anaconda.org/conda-forge/linux-64/r-rcppgsl-0.3.13-r43h40eab2e_2.conda#801638148b5283305ea4ba20f299ac71 +https://conda.anaconda.org/conda-forge/linux-64/r-gam-1.22_4-r43hc4980d5_0.conda#2e188add1ed2e413e362c6ef9795a980 +https://conda.anaconda.org/conda-forge/noarch/r-gtable-0.3.5-r43hc72bb7e_1.conda#373d1655e4d3c45b6abe455d8a52b14e +https://conda.anaconda.org/conda-forge/linux-64/r-mgcv-1.9_1-r43h0d28552_1.conda#154d840fb734a3f80a5ef623b52ff6cd +https://conda.anaconda.org/conda-forge/noarch/r-scales-1.3.0-r43hc72bb7e_1.conda#119d9c10dc652ac1492fc49951d86860 +https://conda.anaconda.org/conda-forge/linux-64/r-vctrs-0.6.5-r43h0d4f4ea_1.conda#7f4c30bb576acec2a682c40790c2d406 +https://conda.anaconda.org/conda-forge/noarch/r-pillar-1.9.0-r43hc72bb7e_2.conda#49a43daa7f46eecd9d42f1073da96662 +https://conda.anaconda.org/conda-forge/linux-64/r-tibble-3.2.1-r43hdb488b9_3.conda#3e78c6ee2205ef56c165cbf2c166fdf6 +https://conda.anaconda.org/conda-forge/noarch/r-ggplot2-3.5.1-r43hc72bb7e_1.conda#a828d1513cabc43cf0711ee0eaec53b2 https://conda.anaconda.org/bioconda/noarch/mapdamage2-2.2.2-pyr43hdfd78af_0.tar.bz2#a0b4b4c6249e00a9876c10200896210e diff --git a/bio/mapdamage2/environment.yaml b/bio/mapdamage2/environment.yaml index ec13b45b5ab..c5af2bce126 100644 --- a/bio/mapdamage2/environment.yaml +++ b/bio/mapdamage2/environment.yaml @@ -4,5 +4,5 @@ channels: - nodefaults dependencies: - mapdamage2 =2.2.2 - - python =3.12.4 + - python =3.12.5 - pysam =0.22.1 From e7fb075ad006c26c407927f37fe6c0e40b15336e Mon Sep 17 00:00:00 2001 From: "snakedeploy-bot[bot]" <115615832+snakedeploy-bot[bot]@users.noreply.github.com> Date: Fri, 9 Aug 2024 05:09:37 +0000 Subject: [PATCH 34/62] perf: autobump bio/spades/metaspades (#3110) Automatic bump of bio/spades/metaspades. --------- Co-authored-by: snakedeploy-bot[bot] <115615832+snakedeploy-bot[bot]@users.noreply.github.com> --- .../metaspades/environment.linux-64.pin.txt | 26 +++++++++---------- bio/spades/metaspades/environment.yaml | 2 +- 2 files changed, 14 insertions(+), 14 deletions(-) diff --git a/bio/spades/metaspades/environment.linux-64.pin.txt b/bio/spades/metaspades/environment.linux-64.pin.txt index 1c8765c3c59..09890cd81de 100644 --- a/bio/spades/metaspades/environment.linux-64.pin.txt +++ b/bio/spades/metaspades/environment.linux-64.pin.txt @@ -3,31 +3,31 @@ # platform: linux-64 @EXPLICIT https://conda.anaconda.org/conda-forge/linux-64/_libgcc_mutex-0.1-conda_forge.tar.bz2#d7c89558ba9fa0495403155b64376d81 -https://conda.anaconda.org/conda-forge/noarch/_sysroot_linux-64_curr_repodata_hack-3-h69a702a_14.conda#38d211c448a67f12fe693fe25df4da23 -https://conda.anaconda.org/conda-forge/linux-64/ca-certificates-2024.6.2-hbcca054_0.conda#847c3c2905cc467cea52c24f9cfa8080 +https://conda.anaconda.org/conda-forge/noarch/_sysroot_linux-64_curr_repodata_hack-3-h69a702a_16.conda#1c005af0c6ff22814b7c52ee448d4bea +https://conda.anaconda.org/conda-forge/linux-64/ca-certificates-2024.7.4-hbcca054_0.conda#23ab7665c5f63cfb9f1f6195256daac6 https://conda.anaconda.org/conda-forge/linux-64/ld_impl_linux-64-2.40-hf3520f5_7.conda#b80f2f396ca2c28b8c14c437a4ed1e74 https://conda.anaconda.org/conda-forge/noarch/tzdata-2024a-h0c530f3_0.conda#161081fc7cec0bfda0d86d7cb595f8d8 -https://conda.anaconda.org/conda-forge/noarch/kernel-headers_linux-64-3.10.0-h4a8ded7_14.conda#f6c14886b1695a2462d296176e831080 -https://conda.anaconda.org/conda-forge/linux-64/libgomp-13.2.0-h77fa898_11.conda#8c462ced2af33648195dc9459f331f31 +https://conda.anaconda.org/conda-forge/noarch/kernel-headers_linux-64-3.10.0-h4a8ded7_16.conda#ff7f38675b226cfb855aebfc32a13e31 +https://conda.anaconda.org/conda-forge/linux-64/libgomp-14.1.0-h77fa898_0.conda#ae061a5ed5f05818acdf9adab72c146d https://conda.anaconda.org/conda-forge/linux-64/_openmp_mutex-4.5-2_gnu.tar.bz2#73aaf86a425cc6e73fcf236a5a46396d -https://conda.anaconda.org/conda-forge/noarch/sysroot_linux-64-2.17-h4a8ded7_14.conda#d5f7a1cca06f56e6ac2b525f199f9b9e -https://conda.anaconda.org/conda-forge/linux-64/libgcc-ng-13.2.0-h77fa898_11.conda#0b3b218a596bb4c3854cc9ee799f94e5 -https://conda.anaconda.org/conda-forge/linux-64/bzip2-1.0.8-hd590300_5.conda#69b8b6202a07720f448be700e300ccf4 +https://conda.anaconda.org/conda-forge/noarch/sysroot_linux-64-2.17-h4a8ded7_16.conda#223fe8a3ff6d5e78484a9d58eb34d055 +https://conda.anaconda.org/conda-forge/linux-64/libgcc-ng-14.1.0-h77fa898_0.conda#ca0fad6a41ddaef54a153b78eccb5037 +https://conda.anaconda.org/conda-forge/linux-64/bzip2-1.0.8-h4bc722e_7.conda#62ee74e96c5ebb0af99386de58cf9553 https://conda.anaconda.org/conda-forge/linux-64/libexpat-2.6.2-h59595ed_0.conda#e7ba12deb7020dd080c6c70e7b6f6a3d https://conda.anaconda.org/conda-forge/linux-64/libffi-3.4.2-h7f98852_5.tar.bz2#d645c6d2ac96843a2bfaccd2d62b3ac3 https://conda.anaconda.org/conda-forge/linux-64/libnsl-2.0.1-hd590300_0.conda#30fd6e37fe21f86f4bd26d6ee73eeec7 -https://conda.anaconda.org/conda-forge/linux-64/libstdcxx-ng-13.2.0-hc0a3c3a_11.conda#eaa8ea74083fb4a78ae19e431e556003 +https://conda.anaconda.org/conda-forge/linux-64/libstdcxx-ng-14.1.0-hc0a3c3a_0.conda#1cb187a157136398ddbaae90713e2498 https://conda.anaconda.org/conda-forge/linux-64/libuuid-2.38.1-h0b41bf4_0.conda#40b61aab5c7ba9ff276c41cfffe6b80b https://conda.anaconda.org/conda-forge/linux-64/libxcrypt-4.4.36-hd590300_1.conda#5aa797f8787fe7a17d1b0821485b5adc https://conda.anaconda.org/conda-forge/linux-64/libzlib-1.3.1-h4ab18f5_1.conda#57d7dc60e9325e3de37ff8dffd18e814 https://conda.anaconda.org/conda-forge/linux-64/ncurses-6.5-h59595ed_0.conda#fcea371545eda051b6deafb24889fc69 -https://conda.anaconda.org/conda-forge/linux-64/openssl-3.3.1-h4ab18f5_0.conda#a41fa0e391cc9e0d6b78ac69ca047a6c +https://conda.anaconda.org/conda-forge/linux-64/openssl-3.3.1-h4bc722e_2.conda#e1b454497f9f7c1147fdde4b53f1b512 https://conda.anaconda.org/conda-forge/linux-64/xz-5.2.6-h166bdaf_0.tar.bz2#2161070d867d1b1204ea749c8eec4ef0 https://conda.anaconda.org/conda-forge/linux-64/libsqlite-3.46.0-hde9e2c9_0.conda#18aa975d2094c34aef978060ae7da7d8 https://conda.anaconda.org/conda-forge/linux-64/readline-8.2-h8228510_1.conda#47d31b792659ce70f470b5c82fdfb7a4 https://conda.anaconda.org/conda-forge/linux-64/tk-8.6.13-noxft_h4845f30_101.conda#d453b98d9c83e71da0741bb0ff4d76bc -https://conda.anaconda.org/conda-forge/linux-64/python-3.12.4-h194c7f8_0_cpython.conda#d73490214f536cccb5819e9873048c92 -https://conda.anaconda.org/conda-forge/noarch/setuptools-70.1.0-pyhd8ed1ab_0.conda#258e66f95f814d51ada2a1fe9274039b +https://conda.anaconda.org/conda-forge/linux-64/python-3.12.5-h2ad013b_0_cpython.conda#9c56c4df45f6571b13111d8df2448692 +https://conda.anaconda.org/conda-forge/noarch/setuptools-72.1.0-pyhd8ed1ab_0.conda#e06d4c26df4f958a8d38696f2c344d15 https://conda.anaconda.org/bioconda/linux-64/spades-4.0.0-h5fb382e_2.tar.bz2#a022789b131c832c2a564cea8b5c8822 -https://conda.anaconda.org/conda-forge/noarch/wheel-0.43.0-pyhd8ed1ab_1.conda#0b5293a157c2b5cd513dd1b03d8d3aae -https://conda.anaconda.org/conda-forge/noarch/pip-24.0-pyhd8ed1ab_0.conda#f586ac1e56c8638b64f9c8122a7b8a67 +https://conda.anaconda.org/conda-forge/noarch/wheel-0.44.0-pyhd8ed1ab_0.conda#d44e3b085abcaef02983c6305b84b584 +https://conda.anaconda.org/conda-forge/noarch/pip-24.2-pyhd8ed1ab_0.conda#6721aef6bfe5937abe70181545dd2c51 diff --git a/bio/spades/metaspades/environment.yaml b/bio/spades/metaspades/environment.yaml index b970c8d5e36..a7b879971c5 100644 --- a/bio/spades/metaspades/environment.yaml +++ b/bio/spades/metaspades/environment.yaml @@ -4,4 +4,4 @@ channels: - nodefaults dependencies: - spades =4.0.0 - - python =3.12.4 + - python =3.12.5 From 5ec4df572af0fed2589579cd4bc7be8749d55886 Mon Sep 17 00:00:00 2001 From: "snakedeploy-bot[bot]" <115615832+snakedeploy-bot[bot]@users.noreply.github.com> Date: Fri, 9 Aug 2024 05:32:24 +0000 Subject: [PATCH 35/62] perf: autobump bio/vembrane/filter (#3111) Automatic bump of bio/vembrane/filter. --------- Co-authored-by: snakedeploy-bot[bot] <115615832+snakedeploy-bot[bot]@users.noreply.github.com> --- .../filter/environment.linux-64.pin.txt | 46 +++++++++---------- bio/vembrane/filter/environment.yaml | 2 +- 2 files changed, 24 insertions(+), 24 deletions(-) diff --git a/bio/vembrane/filter/environment.linux-64.pin.txt b/bio/vembrane/filter/environment.linux-64.pin.txt index 2ad5e45f237..9e9677adbf9 100644 --- a/bio/vembrane/filter/environment.linux-64.pin.txt +++ b/bio/vembrane/filter/environment.linux-64.pin.txt @@ -3,51 +3,51 @@ # platform: linux-64 @EXPLICIT https://conda.anaconda.org/conda-forge/linux-64/_libgcc_mutex-0.1-conda_forge.tar.bz2#d7c89558ba9fa0495403155b64376d81 -https://conda.anaconda.org/conda-forge/linux-64/ca-certificates-2024.2.2-hbcca054_0.conda#2f4327a1cbe7f022401b236e915a5fef -https://conda.anaconda.org/conda-forge/linux-64/ld_impl_linux-64-2.40-h41732ed_0.conda#7aca3059a1729aa76c597603f10b0dd3 -https://conda.anaconda.org/conda-forge/linux-64/libstdcxx-ng-13.2.0-h7e041cc_5.conda#f6f6600d18a4047b54f803cf708b868a +https://conda.anaconda.org/conda-forge/linux-64/ca-certificates-2024.7.4-hbcca054_0.conda#23ab7665c5f63cfb9f1f6195256daac6 +https://conda.anaconda.org/conda-forge/linux-64/ld_impl_linux-64-2.40-hf3520f5_7.conda#b80f2f396ca2c28b8c14c437a4ed1e74 https://conda.anaconda.org/conda-forge/linux-64/python_abi-3.10-4_cp310.conda#26322ec5d7712c3ded99dd656142b8ce https://conda.anaconda.org/conda-forge/noarch/tzdata-2024a-h0c530f3_0.conda#161081fc7cec0bfda0d86d7cb595f8d8 -https://conda.anaconda.org/conda-forge/linux-64/libgomp-13.2.0-h807b86a_5.conda#d211c42b9ce49aee3734fdc828731689 +https://conda.anaconda.org/conda-forge/linux-64/libgomp-14.1.0-h77fa898_0.conda#ae061a5ed5f05818acdf9adab72c146d https://conda.anaconda.org/conda-forge/linux-64/_openmp_mutex-4.5-2_gnu.tar.bz2#73aaf86a425cc6e73fcf236a5a46396d -https://conda.anaconda.org/conda-forge/linux-64/libgcc-ng-13.2.0-h807b86a_5.conda#d4ff227c46917d3b4565302a2bbb276b -https://conda.anaconda.org/conda-forge/linux-64/bzip2-1.0.8-hd590300_5.conda#69b8b6202a07720f448be700e300ccf4 -https://conda.anaconda.org/conda-forge/linux-64/c-ares-1.27.0-hd590300_0.conda#f6afff0e9ee08d2f1b897881a4f38cdb +https://conda.anaconda.org/conda-forge/linux-64/libgcc-ng-14.1.0-h77fa898_0.conda#ca0fad6a41ddaef54a153b78eccb5037 +https://conda.anaconda.org/conda-forge/linux-64/bzip2-1.0.8-h4bc722e_7.conda#62ee74e96c5ebb0af99386de58cf9553 +https://conda.anaconda.org/conda-forge/linux-64/c-ares-1.32.3-h4bc722e_0.conda#7624e34ee6baebfc80d67bac76cc9d9d https://conda.anaconda.org/conda-forge/linux-64/keyutils-1.6.1-h166bdaf_0.tar.bz2#30186d27e2c9fa62b45fb1476b7200e3 -https://conda.anaconda.org/conda-forge/linux-64/libdeflate-1.13-h166bdaf_0.tar.bz2#4b5bee2e957570197327d0b20a718891 +https://conda.anaconda.org/conda-forge/linux-64/libdeflate-1.21-h4bc722e_0.conda#36ce76665bf67f5aac36be7a0d21b7f3 https://conda.anaconda.org/conda-forge/linux-64/libev-4.33-hd590300_2.conda#172bf1cd1ff8629f2b1179945ed45055 https://conda.anaconda.org/conda-forge/linux-64/libffi-3.4.2-h7f98852_5.tar.bz2#d645c6d2ac96843a2bfaccd2d62b3ac3 -https://conda.anaconda.org/conda-forge/linux-64/libgfortran5-13.2.0-ha4646dd_5.conda#7a6bd7a12a4bd359e2afe6c0fa1acace +https://conda.anaconda.org/conda-forge/linux-64/libgfortran5-14.1.0-hc5f4f2c_0.conda#6456c2620c990cd8dde2428a27ba0bc5 https://conda.anaconda.org/conda-forge/linux-64/libnsl-2.0.1-hd590300_0.conda#30fd6e37fe21f86f4bd26d6ee73eeec7 +https://conda.anaconda.org/conda-forge/linux-64/libstdcxx-ng-14.1.0-hc0a3c3a_0.conda#1cb187a157136398ddbaae90713e2498 https://conda.anaconda.org/conda-forge/linux-64/libuuid-2.38.1-h0b41bf4_0.conda#40b61aab5c7ba9ff276c41cfffe6b80b -https://conda.anaconda.org/conda-forge/linux-64/libzlib-1.2.13-hd590300_5.conda#f36c115f1ee199da648e0597ec2047ad -https://conda.anaconda.org/conda-forge/linux-64/ncurses-6.4.20240210-h59595ed_0.conda#97da8860a0da5413c7c98a3b3838a645 +https://conda.anaconda.org/conda-forge/linux-64/libzlib-1.2.13-h4ab18f5_6.conda#27329162c0dc732bcf67a4e0cd488125 +https://conda.anaconda.org/conda-forge/linux-64/ncurses-6.5-h59595ed_0.conda#fcea371545eda051b6deafb24889fc69 https://conda.anaconda.org/conda-forge/linux-64/openssl-1.1.1w-hd590300_0.conda#301e70057a3bd399640bb16bbdf87995 https://conda.anaconda.org/conda-forge/linux-64/xz-5.2.6-h166bdaf_0.tar.bz2#2161070d867d1b1204ea749c8eec4ef0 https://conda.anaconda.org/conda-forge/linux-64/yaml-0.2.5-h7f98852_2.tar.bz2#4cb3ad778ec2d5a7acbdf254eb1c42ae https://conda.anaconda.org/conda-forge/linux-64/libedit-3.1.20191231-he28a2e2_2.tar.bz2#4d331e44109e3f0e19b4cb8f9b82f3e1 -https://conda.anaconda.org/conda-forge/linux-64/libgfortran-ng-13.2.0-h69a702a_5.conda#e73e9cfd1191783392131e6238bdb3e9 +https://conda.anaconda.org/conda-forge/linux-64/libgfortran-ng-14.1.0-h69a702a_0.conda#f4ca84fbd6d06b0a052fb2d5b96dde41 https://conda.anaconda.org/conda-forge/linux-64/libnghttp2-1.51.0-hdcd2b5c_0.conda#c42b460bae0365fb9777b1ff9d09a554 -https://conda.anaconda.org/conda-forge/linux-64/libsqlite-3.45.2-h2797004_0.conda#866983a220e27a80cb75e85cb30466a1 +https://conda.anaconda.org/conda-forge/linux-64/libsqlite-3.46.0-hde9e2c9_0.conda#18aa975d2094c34aef978060ae7da7d8 https://conda.anaconda.org/conda-forge/linux-64/libssh2-1.10.0-haa6b8db_3.tar.bz2#89acee135f0809a18a1f4537390aa2dd https://conda.anaconda.org/conda-forge/linux-64/readline-8.2-h8228510_1.conda#47d31b792659ce70f470b5c82fdfb7a4 https://conda.anaconda.org/conda-forge/linux-64/tk-8.6.13-noxft_h4845f30_101.conda#d453b98d9c83e71da0741bb0ff4d76bc -https://conda.anaconda.org/conda-forge/linux-64/zlib-1.2.13-hd590300_5.conda#68c34ec6149623be41a1933ab996a209 +https://conda.anaconda.org/conda-forge/linux-64/zlib-1.2.13-h4ab18f5_6.conda#559d338a4234c2ad6e676f460a093e67 https://conda.anaconda.org/conda-forge/linux-64/krb5-1.20.1-hf9c8cef_0.conda#5f7e9efd540d7ac4b485660231ba6150 -https://conda.anaconda.org/conda-forge/linux-64/libopenblas-0.3.26-pthreads_h413a1c8_0.conda#760ae35415f5ba8b15d09df5afe8b23a +https://conda.anaconda.org/conda-forge/linux-64/libopenblas-0.3.27-pthreads_hac2b453_1.conda#ae05ece66d3924ac3d48b4aa3fa96cec https://conda.anaconda.org/conda-forge/linux-64/python-3.10.8-h257c98d_0_cpython.conda#fa742265350d7f6d664bc13436caf4ad -https://conda.anaconda.org/conda-forge/linux-64/libblas-3.9.0-21_linux64_openblas.conda#0ac9f44fc096772b0aa092119b00c3ca +https://conda.anaconda.org/conda-forge/linux-64/libblas-3.9.0-23_linux64_openblas.conda#96c8450a40aa2b9733073a9460de972c https://conda.anaconda.org/conda-forge/linux-64/libcurl-7.87.0-h6312ad2_0.conda#ad07f06bd133e76e12165bc3ec2c8646 -https://conda.anaconda.org/conda-forge/linux-64/pyyaml-6.0.1-py310h2372a71_1.conda#bb010e368de4940771368bc3dc4c63e7 -https://conda.anaconda.org/conda-forge/noarch/setuptools-69.2.0-pyhd8ed1ab_0.conda#da214ecd521a720a9d521c68047682dc +https://conda.anaconda.org/conda-forge/linux-64/pyyaml-6.0.2-py310h5b4e0ec_0.conda#ad8de7b4ac482217959cc1e8fe0cc56d +https://conda.anaconda.org/conda-forge/noarch/setuptools-72.1.0-pyhd8ed1ab_0.conda#e06d4c26df4f958a8d38696f2c344d15 https://conda.anaconda.org/conda-forge/noarch/six-1.16.0-pyh6c4a22f_0.tar.bz2#e5f25f8dbc060e9a8d912e432202afc2 https://conda.anaconda.org/conda-forge/noarch/sortedcontainers-2.4.0-pyhd8ed1ab_0.tar.bz2#6d6552722448103793743dabfbda532d -https://conda.anaconda.org/conda-forge/noarch/wheel-0.43.0-pyhd8ed1ab_1.conda#0b5293a157c2b5cd513dd1b03d8d3aae +https://conda.anaconda.org/conda-forge/noarch/wheel-0.44.0-pyhd8ed1ab_0.conda#d44e3b085abcaef02983c6305b84b584 https://conda.anaconda.org/conda-forge/noarch/asttokens-2.4.1-pyhd8ed1ab_0.conda#5f25798dcefd8252ce5f9dc494d5f571 https://conda.anaconda.org/conda-forge/noarch/intervaltree-3.1.0-pyhd8ed1ab_1.conda#e32bb5b0369e819c4dde653d4c4572f3 -https://conda.anaconda.org/conda-forge/linux-64/libcblas-3.9.0-21_linux64_openblas.conda#4a3816d06451c4946e2db26b86472cb6 -https://conda.anaconda.org/conda-forge/linux-64/liblapack-3.9.0-21_linux64_openblas.conda#1a42f305615c3867684e049e85927531 -https://conda.anaconda.org/conda-forge/noarch/pip-24.0-pyhd8ed1ab_0.conda#f586ac1e56c8638b64f9c8122a7b8a67 +https://conda.anaconda.org/conda-forge/linux-64/libcblas-3.9.0-23_linux64_openblas.conda#eede29b40efa878cbe5bdcb767e97310 +https://conda.anaconda.org/conda-forge/linux-64/liblapack-3.9.0-23_linux64_openblas.conda#2af0879961951987e464722fd00ec1e0 +https://conda.anaconda.org/conda-forge/noarch/pip-24.2-pyhd8ed1ab_0.conda#6721aef6bfe5937abe70181545dd2c51 https://conda.anaconda.org/bioconda/linux-64/pysam-0.20.0-py310hff46b53_0.tar.bz2#3bd14dade02bfaaf4512c27ebb879e31 https://conda.anaconda.org/conda-forge/linux-64/numpy-1.26.4-py310hb13e2d6_0.conda#6593de64c935768b6bad3e19b3e978be -https://conda.anaconda.org/bioconda/noarch/vembrane-1.0.5-pyhdfd78af_0.tar.bz2#2aa11421f68bb9b7e09b95538fdb0b3b +https://conda.anaconda.org/bioconda/noarch/vembrane-1.0.6-pyhdfd78af_0.tar.bz2#24be610f750da947a19886560796b26d diff --git a/bio/vembrane/filter/environment.yaml b/bio/vembrane/filter/environment.yaml index be8f295d926..5e8b8538456 100644 --- a/bio/vembrane/filter/environment.yaml +++ b/bio/vembrane/filter/environment.yaml @@ -4,4 +4,4 @@ channels: - default - nodefaults dependencies: - - vembrane =1.0.5 + - vembrane =1.0.6 From 9411cc94ed21493c62cc4fcd27307a87fe205e34 Mon Sep 17 00:00:00 2001 From: "snakedeploy-bot[bot]" <115615832+snakedeploy-bot[bot]@users.noreply.github.com> Date: Fri, 9 Aug 2024 05:38:29 +0000 Subject: [PATCH 36/62] perf: autobump bio/vembrane/table (#3112) Automatic bump of bio/vembrane/table. --------- Co-authored-by: snakedeploy-bot[bot] <115615832+snakedeploy-bot[bot]@users.noreply.github.com> --- .../table/environment.linux-64.pin.txt | 46 +++++++++---------- bio/vembrane/table/environment.yaml | 2 +- 2 files changed, 24 insertions(+), 24 deletions(-) diff --git a/bio/vembrane/table/environment.linux-64.pin.txt b/bio/vembrane/table/environment.linux-64.pin.txt index 2ad5e45f237..9e9677adbf9 100644 --- a/bio/vembrane/table/environment.linux-64.pin.txt +++ b/bio/vembrane/table/environment.linux-64.pin.txt @@ -3,51 +3,51 @@ # platform: linux-64 @EXPLICIT https://conda.anaconda.org/conda-forge/linux-64/_libgcc_mutex-0.1-conda_forge.tar.bz2#d7c89558ba9fa0495403155b64376d81 -https://conda.anaconda.org/conda-forge/linux-64/ca-certificates-2024.2.2-hbcca054_0.conda#2f4327a1cbe7f022401b236e915a5fef -https://conda.anaconda.org/conda-forge/linux-64/ld_impl_linux-64-2.40-h41732ed_0.conda#7aca3059a1729aa76c597603f10b0dd3 -https://conda.anaconda.org/conda-forge/linux-64/libstdcxx-ng-13.2.0-h7e041cc_5.conda#f6f6600d18a4047b54f803cf708b868a +https://conda.anaconda.org/conda-forge/linux-64/ca-certificates-2024.7.4-hbcca054_0.conda#23ab7665c5f63cfb9f1f6195256daac6 +https://conda.anaconda.org/conda-forge/linux-64/ld_impl_linux-64-2.40-hf3520f5_7.conda#b80f2f396ca2c28b8c14c437a4ed1e74 https://conda.anaconda.org/conda-forge/linux-64/python_abi-3.10-4_cp310.conda#26322ec5d7712c3ded99dd656142b8ce https://conda.anaconda.org/conda-forge/noarch/tzdata-2024a-h0c530f3_0.conda#161081fc7cec0bfda0d86d7cb595f8d8 -https://conda.anaconda.org/conda-forge/linux-64/libgomp-13.2.0-h807b86a_5.conda#d211c42b9ce49aee3734fdc828731689 +https://conda.anaconda.org/conda-forge/linux-64/libgomp-14.1.0-h77fa898_0.conda#ae061a5ed5f05818acdf9adab72c146d https://conda.anaconda.org/conda-forge/linux-64/_openmp_mutex-4.5-2_gnu.tar.bz2#73aaf86a425cc6e73fcf236a5a46396d -https://conda.anaconda.org/conda-forge/linux-64/libgcc-ng-13.2.0-h807b86a_5.conda#d4ff227c46917d3b4565302a2bbb276b -https://conda.anaconda.org/conda-forge/linux-64/bzip2-1.0.8-hd590300_5.conda#69b8b6202a07720f448be700e300ccf4 -https://conda.anaconda.org/conda-forge/linux-64/c-ares-1.27.0-hd590300_0.conda#f6afff0e9ee08d2f1b897881a4f38cdb +https://conda.anaconda.org/conda-forge/linux-64/libgcc-ng-14.1.0-h77fa898_0.conda#ca0fad6a41ddaef54a153b78eccb5037 +https://conda.anaconda.org/conda-forge/linux-64/bzip2-1.0.8-h4bc722e_7.conda#62ee74e96c5ebb0af99386de58cf9553 +https://conda.anaconda.org/conda-forge/linux-64/c-ares-1.32.3-h4bc722e_0.conda#7624e34ee6baebfc80d67bac76cc9d9d https://conda.anaconda.org/conda-forge/linux-64/keyutils-1.6.1-h166bdaf_0.tar.bz2#30186d27e2c9fa62b45fb1476b7200e3 -https://conda.anaconda.org/conda-forge/linux-64/libdeflate-1.13-h166bdaf_0.tar.bz2#4b5bee2e957570197327d0b20a718891 +https://conda.anaconda.org/conda-forge/linux-64/libdeflate-1.21-h4bc722e_0.conda#36ce76665bf67f5aac36be7a0d21b7f3 https://conda.anaconda.org/conda-forge/linux-64/libev-4.33-hd590300_2.conda#172bf1cd1ff8629f2b1179945ed45055 https://conda.anaconda.org/conda-forge/linux-64/libffi-3.4.2-h7f98852_5.tar.bz2#d645c6d2ac96843a2bfaccd2d62b3ac3 -https://conda.anaconda.org/conda-forge/linux-64/libgfortran5-13.2.0-ha4646dd_5.conda#7a6bd7a12a4bd359e2afe6c0fa1acace +https://conda.anaconda.org/conda-forge/linux-64/libgfortran5-14.1.0-hc5f4f2c_0.conda#6456c2620c990cd8dde2428a27ba0bc5 https://conda.anaconda.org/conda-forge/linux-64/libnsl-2.0.1-hd590300_0.conda#30fd6e37fe21f86f4bd26d6ee73eeec7 +https://conda.anaconda.org/conda-forge/linux-64/libstdcxx-ng-14.1.0-hc0a3c3a_0.conda#1cb187a157136398ddbaae90713e2498 https://conda.anaconda.org/conda-forge/linux-64/libuuid-2.38.1-h0b41bf4_0.conda#40b61aab5c7ba9ff276c41cfffe6b80b -https://conda.anaconda.org/conda-forge/linux-64/libzlib-1.2.13-hd590300_5.conda#f36c115f1ee199da648e0597ec2047ad -https://conda.anaconda.org/conda-forge/linux-64/ncurses-6.4.20240210-h59595ed_0.conda#97da8860a0da5413c7c98a3b3838a645 +https://conda.anaconda.org/conda-forge/linux-64/libzlib-1.2.13-h4ab18f5_6.conda#27329162c0dc732bcf67a4e0cd488125 +https://conda.anaconda.org/conda-forge/linux-64/ncurses-6.5-h59595ed_0.conda#fcea371545eda051b6deafb24889fc69 https://conda.anaconda.org/conda-forge/linux-64/openssl-1.1.1w-hd590300_0.conda#301e70057a3bd399640bb16bbdf87995 https://conda.anaconda.org/conda-forge/linux-64/xz-5.2.6-h166bdaf_0.tar.bz2#2161070d867d1b1204ea749c8eec4ef0 https://conda.anaconda.org/conda-forge/linux-64/yaml-0.2.5-h7f98852_2.tar.bz2#4cb3ad778ec2d5a7acbdf254eb1c42ae https://conda.anaconda.org/conda-forge/linux-64/libedit-3.1.20191231-he28a2e2_2.tar.bz2#4d331e44109e3f0e19b4cb8f9b82f3e1 -https://conda.anaconda.org/conda-forge/linux-64/libgfortran-ng-13.2.0-h69a702a_5.conda#e73e9cfd1191783392131e6238bdb3e9 +https://conda.anaconda.org/conda-forge/linux-64/libgfortran-ng-14.1.0-h69a702a_0.conda#f4ca84fbd6d06b0a052fb2d5b96dde41 https://conda.anaconda.org/conda-forge/linux-64/libnghttp2-1.51.0-hdcd2b5c_0.conda#c42b460bae0365fb9777b1ff9d09a554 -https://conda.anaconda.org/conda-forge/linux-64/libsqlite-3.45.2-h2797004_0.conda#866983a220e27a80cb75e85cb30466a1 +https://conda.anaconda.org/conda-forge/linux-64/libsqlite-3.46.0-hde9e2c9_0.conda#18aa975d2094c34aef978060ae7da7d8 https://conda.anaconda.org/conda-forge/linux-64/libssh2-1.10.0-haa6b8db_3.tar.bz2#89acee135f0809a18a1f4537390aa2dd https://conda.anaconda.org/conda-forge/linux-64/readline-8.2-h8228510_1.conda#47d31b792659ce70f470b5c82fdfb7a4 https://conda.anaconda.org/conda-forge/linux-64/tk-8.6.13-noxft_h4845f30_101.conda#d453b98d9c83e71da0741bb0ff4d76bc -https://conda.anaconda.org/conda-forge/linux-64/zlib-1.2.13-hd590300_5.conda#68c34ec6149623be41a1933ab996a209 +https://conda.anaconda.org/conda-forge/linux-64/zlib-1.2.13-h4ab18f5_6.conda#559d338a4234c2ad6e676f460a093e67 https://conda.anaconda.org/conda-forge/linux-64/krb5-1.20.1-hf9c8cef_0.conda#5f7e9efd540d7ac4b485660231ba6150 -https://conda.anaconda.org/conda-forge/linux-64/libopenblas-0.3.26-pthreads_h413a1c8_0.conda#760ae35415f5ba8b15d09df5afe8b23a +https://conda.anaconda.org/conda-forge/linux-64/libopenblas-0.3.27-pthreads_hac2b453_1.conda#ae05ece66d3924ac3d48b4aa3fa96cec https://conda.anaconda.org/conda-forge/linux-64/python-3.10.8-h257c98d_0_cpython.conda#fa742265350d7f6d664bc13436caf4ad -https://conda.anaconda.org/conda-forge/linux-64/libblas-3.9.0-21_linux64_openblas.conda#0ac9f44fc096772b0aa092119b00c3ca +https://conda.anaconda.org/conda-forge/linux-64/libblas-3.9.0-23_linux64_openblas.conda#96c8450a40aa2b9733073a9460de972c https://conda.anaconda.org/conda-forge/linux-64/libcurl-7.87.0-h6312ad2_0.conda#ad07f06bd133e76e12165bc3ec2c8646 -https://conda.anaconda.org/conda-forge/linux-64/pyyaml-6.0.1-py310h2372a71_1.conda#bb010e368de4940771368bc3dc4c63e7 -https://conda.anaconda.org/conda-forge/noarch/setuptools-69.2.0-pyhd8ed1ab_0.conda#da214ecd521a720a9d521c68047682dc +https://conda.anaconda.org/conda-forge/linux-64/pyyaml-6.0.2-py310h5b4e0ec_0.conda#ad8de7b4ac482217959cc1e8fe0cc56d +https://conda.anaconda.org/conda-forge/noarch/setuptools-72.1.0-pyhd8ed1ab_0.conda#e06d4c26df4f958a8d38696f2c344d15 https://conda.anaconda.org/conda-forge/noarch/six-1.16.0-pyh6c4a22f_0.tar.bz2#e5f25f8dbc060e9a8d912e432202afc2 https://conda.anaconda.org/conda-forge/noarch/sortedcontainers-2.4.0-pyhd8ed1ab_0.tar.bz2#6d6552722448103793743dabfbda532d -https://conda.anaconda.org/conda-forge/noarch/wheel-0.43.0-pyhd8ed1ab_1.conda#0b5293a157c2b5cd513dd1b03d8d3aae +https://conda.anaconda.org/conda-forge/noarch/wheel-0.44.0-pyhd8ed1ab_0.conda#d44e3b085abcaef02983c6305b84b584 https://conda.anaconda.org/conda-forge/noarch/asttokens-2.4.1-pyhd8ed1ab_0.conda#5f25798dcefd8252ce5f9dc494d5f571 https://conda.anaconda.org/conda-forge/noarch/intervaltree-3.1.0-pyhd8ed1ab_1.conda#e32bb5b0369e819c4dde653d4c4572f3 -https://conda.anaconda.org/conda-forge/linux-64/libcblas-3.9.0-21_linux64_openblas.conda#4a3816d06451c4946e2db26b86472cb6 -https://conda.anaconda.org/conda-forge/linux-64/liblapack-3.9.0-21_linux64_openblas.conda#1a42f305615c3867684e049e85927531 -https://conda.anaconda.org/conda-forge/noarch/pip-24.0-pyhd8ed1ab_0.conda#f586ac1e56c8638b64f9c8122a7b8a67 +https://conda.anaconda.org/conda-forge/linux-64/libcblas-3.9.0-23_linux64_openblas.conda#eede29b40efa878cbe5bdcb767e97310 +https://conda.anaconda.org/conda-forge/linux-64/liblapack-3.9.0-23_linux64_openblas.conda#2af0879961951987e464722fd00ec1e0 +https://conda.anaconda.org/conda-forge/noarch/pip-24.2-pyhd8ed1ab_0.conda#6721aef6bfe5937abe70181545dd2c51 https://conda.anaconda.org/bioconda/linux-64/pysam-0.20.0-py310hff46b53_0.tar.bz2#3bd14dade02bfaaf4512c27ebb879e31 https://conda.anaconda.org/conda-forge/linux-64/numpy-1.26.4-py310hb13e2d6_0.conda#6593de64c935768b6bad3e19b3e978be -https://conda.anaconda.org/bioconda/noarch/vembrane-1.0.5-pyhdfd78af_0.tar.bz2#2aa11421f68bb9b7e09b95538fdb0b3b +https://conda.anaconda.org/bioconda/noarch/vembrane-1.0.6-pyhdfd78af_0.tar.bz2#24be610f750da947a19886560796b26d diff --git a/bio/vembrane/table/environment.yaml b/bio/vembrane/table/environment.yaml index be8f295d926..5e8b8538456 100644 --- a/bio/vembrane/table/environment.yaml +++ b/bio/vembrane/table/environment.yaml @@ -4,4 +4,4 @@ channels: - default - nodefaults dependencies: - - vembrane =1.0.5 + - vembrane =1.0.6 From 4e7d29b0aba8e20b2df8754d551de81a4c83fb53 Mon Sep 17 00:00:00 2001 From: "snakedeploy-bot[bot]" <115615832+snakedeploy-bot[bot]@users.noreply.github.com> Date: Fri, 9 Aug 2024 05:41:22 +0000 Subject: [PATCH 37/62] perf: autobump bio/vep/plugins (#3113) Automatic bump of bio/vep/plugins. --------- Co-authored-by: snakedeploy-bot[bot] <115615832+snakedeploy-bot[bot]@users.noreply.github.com> --- bio/vep/plugins/environment.linux-64.pin.txt | 18 +++++++++--------- bio/vep/plugins/environment.yaml | 2 +- 2 files changed, 10 insertions(+), 10 deletions(-) diff --git a/bio/vep/plugins/environment.linux-64.pin.txt b/bio/vep/plugins/environment.linux-64.pin.txt index 4b7d0003a50..13369a66521 100644 --- a/bio/vep/plugins/environment.linux-64.pin.txt +++ b/bio/vep/plugins/environment.linux-64.pin.txt @@ -3,13 +3,13 @@ # platform: linux-64 @EXPLICIT https://conda.anaconda.org/conda-forge/linux-64/_libgcc_mutex-0.1-conda_forge.tar.bz2#d7c89558ba9fa0495403155b64376d81 -https://conda.anaconda.org/conda-forge/linux-64/ca-certificates-2024.6.2-hbcca054_0.conda#847c3c2905cc467cea52c24f9cfa8080 +https://conda.anaconda.org/conda-forge/linux-64/ca-certificates-2024.7.4-hbcca054_0.conda#23ab7665c5f63cfb9f1f6195256daac6 https://conda.anaconda.org/conda-forge/linux-64/ld_impl_linux-64-2.40-hf3520f5_7.conda#b80f2f396ca2c28b8c14c437a4ed1e74 https://conda.anaconda.org/conda-forge/noarch/tzdata-2024a-h0c530f3_0.conda#161081fc7cec0bfda0d86d7cb595f8d8 -https://conda.anaconda.org/conda-forge/linux-64/libgomp-13.2.0-h77fa898_11.conda#8c462ced2af33648195dc9459f331f31 +https://conda.anaconda.org/conda-forge/linux-64/libgomp-14.1.0-h77fa898_0.conda#ae061a5ed5f05818acdf9adab72c146d https://conda.anaconda.org/conda-forge/linux-64/_openmp_mutex-4.5-2_gnu.tar.bz2#73aaf86a425cc6e73fcf236a5a46396d -https://conda.anaconda.org/conda-forge/linux-64/libgcc-ng-13.2.0-h77fa898_11.conda#0b3b218a596bb4c3854cc9ee799f94e5 -https://conda.anaconda.org/conda-forge/linux-64/bzip2-1.0.8-hd590300_5.conda#69b8b6202a07720f448be700e300ccf4 +https://conda.anaconda.org/conda-forge/linux-64/libgcc-ng-14.1.0-h77fa898_0.conda#ca0fad6a41ddaef54a153b78eccb5037 +https://conda.anaconda.org/conda-forge/linux-64/bzip2-1.0.8-h4bc722e_7.conda#62ee74e96c5ebb0af99386de58cf9553 https://conda.anaconda.org/conda-forge/linux-64/libexpat-2.6.2-h59595ed_0.conda#e7ba12deb7020dd080c6c70e7b6f6a3d https://conda.anaconda.org/conda-forge/linux-64/libffi-3.4.2-h7f98852_5.tar.bz2#d645c6d2ac96843a2bfaccd2d62b3ac3 https://conda.anaconda.org/conda-forge/linux-64/libnsl-2.0.1-hd590300_0.conda#30fd6e37fe21f86f4bd26d6ee73eeec7 @@ -17,12 +17,12 @@ https://conda.anaconda.org/conda-forge/linux-64/libuuid-2.38.1-h0b41bf4_0.conda# https://conda.anaconda.org/conda-forge/linux-64/libxcrypt-4.4.36-hd590300_1.conda#5aa797f8787fe7a17d1b0821485b5adc https://conda.anaconda.org/conda-forge/linux-64/libzlib-1.3.1-h4ab18f5_1.conda#57d7dc60e9325e3de37ff8dffd18e814 https://conda.anaconda.org/conda-forge/linux-64/ncurses-6.5-h59595ed_0.conda#fcea371545eda051b6deafb24889fc69 -https://conda.anaconda.org/conda-forge/linux-64/openssl-3.3.1-h4ab18f5_0.conda#a41fa0e391cc9e0d6b78ac69ca047a6c +https://conda.anaconda.org/conda-forge/linux-64/openssl-3.3.1-h4bc722e_2.conda#e1b454497f9f7c1147fdde4b53f1b512 https://conda.anaconda.org/conda-forge/linux-64/xz-5.2.6-h166bdaf_0.tar.bz2#2161070d867d1b1204ea749c8eec4ef0 https://conda.anaconda.org/conda-forge/linux-64/libsqlite-3.46.0-hde9e2c9_0.conda#18aa975d2094c34aef978060ae7da7d8 https://conda.anaconda.org/conda-forge/linux-64/readline-8.2-h8228510_1.conda#47d31b792659ce70f470b5c82fdfb7a4 https://conda.anaconda.org/conda-forge/linux-64/tk-8.6.13-noxft_h4845f30_101.conda#d453b98d9c83e71da0741bb0ff4d76bc -https://conda.anaconda.org/conda-forge/linux-64/python-3.12.4-h194c7f8_0_cpython.conda#d73490214f536cccb5819e9873048c92 -https://conda.anaconda.org/conda-forge/noarch/setuptools-70.1.0-pyhd8ed1ab_0.conda#258e66f95f814d51ada2a1fe9274039b -https://conda.anaconda.org/conda-forge/noarch/wheel-0.43.0-pyhd8ed1ab_1.conda#0b5293a157c2b5cd513dd1b03d8d3aae -https://conda.anaconda.org/conda-forge/noarch/pip-24.0-pyhd8ed1ab_0.conda#f586ac1e56c8638b64f9c8122a7b8a67 +https://conda.anaconda.org/conda-forge/linux-64/python-3.12.5-h2ad013b_0_cpython.conda#9c56c4df45f6571b13111d8df2448692 +https://conda.anaconda.org/conda-forge/noarch/setuptools-72.1.0-pyhd8ed1ab_0.conda#e06d4c26df4f958a8d38696f2c344d15 +https://conda.anaconda.org/conda-forge/noarch/wheel-0.44.0-pyhd8ed1ab_0.conda#d44e3b085abcaef02983c6305b84b584 +https://conda.anaconda.org/conda-forge/noarch/pip-24.2-pyhd8ed1ab_0.conda#6721aef6bfe5937abe70181545dd2c51 diff --git a/bio/vep/plugins/environment.yaml b/bio/vep/plugins/environment.yaml index fbb7c522747..448089eae23 100644 --- a/bio/vep/plugins/environment.yaml +++ b/bio/vep/plugins/environment.yaml @@ -2,4 +2,4 @@ channels: - conda-forge - nodefaults dependencies: - - python =3.12.4 + - python =3.12.5 From 26a097d87ed7c429a3c960bf195a04bd19372899 Mon Sep 17 00:00:00 2001 From: "github-actions[bot]" <41898282+github-actions[bot]@users.noreply.github.com> Date: Fri, 9 Aug 2024 13:19:54 +0200 Subject: [PATCH 38/62] chore: release 3.14.1 (#3097) :robot: I have created a release \*beep\* \*boop\* --- ### [3.14.1](https://www.github.com/snakemake/snakemake-wrappers/compare/v3.14.0...v3.14.1) (2024-08-09) ### Bug Fixes * add missing raw string in REGEX_RULES ([#3104](https://www.github.com/snakemake/snakemake-wrappers/issues/3104)) ([74a3269](https://www.github.com/snakemake/snakemake-wrappers/commit/74a3269fe7152464e8134d7560a32540e4197977)) * download already indexed vep cache tarball ([#3102](https://www.github.com/snakemake/snakemake-wrappers/issues/3102)) ([13c6ef7](https://www.github.com/snakemake/snakemake-wrappers/commit/13c6ef74db8f6c4608c87f6209bab69b3e9ed16a)) ### Performance Improvements * autobump bio/encode_fastq_downloader ([#3105](https://www.github.com/snakemake/snakemake-wrappers/issues/3105)) ([695ab1b](https://www.github.com/snakemake/snakemake-wrappers/commit/695ab1b1e39ec2a9693ef5f721bc564e50f716e2)) * autobump bio/gatk3/indelrealigner ([#3106](https://www.github.com/snakemake/snakemake-wrappers/issues/3106)) ([09d6e0b](https://www.github.com/snakemake/snakemake-wrappers/commit/09d6e0b0d0857c88f6f2c81aec3d7714eb9fb738)) * autobump bio/gdc-api/bam-slicing ([#3096](https://www.github.com/snakemake/snakemake-wrappers/issues/3096)) ([248b611](https://www.github.com/snakemake/snakemake-wrappers/commit/248b611f33ce879ad40eef4b78ad2d84cda43948)) * autobump bio/last/lastal ([#3108](https://www.github.com/snakemake/snakemake-wrappers/issues/3108)) ([9f7a264](https://www.github.com/snakemake/snakemake-wrappers/commit/9f7a264c5ceb560008945a4520960e219f470827)) * autobump bio/last/lastdb ([#3107](https://www.github.com/snakemake/snakemake-wrappers/issues/3107)) ([b1c3334](https://www.github.com/snakemake/snakemake-wrappers/commit/b1c333462d4540a4ed995af2a190bdab0f43e66a)) * autobump bio/mapdamage2 ([#3109](https://www.github.com/snakemake/snakemake-wrappers/issues/3109)) ([a870b8e](https://www.github.com/snakemake/snakemake-wrappers/commit/a870b8ef9bc89a18b093dc6303048b5e1202f740)) * autobump bio/sourmash/compute ([#3098](https://www.github.com/snakemake/snakemake-wrappers/issues/3098)) ([5796bc6](https://www.github.com/snakemake/snakemake-wrappers/commit/5796bc6fe0908c4922bb8bfc93183df72afa04b2)) * autobump bio/spades/metaspades ([#3110](https://www.github.com/snakemake/snakemake-wrappers/issues/3110)) ([e7fb075](https://www.github.com/snakemake/snakemake-wrappers/commit/e7fb075ad006c26c407927f37fe6c0e40b15336e)) * autobump bio/unicycler ([#3099](https://www.github.com/snakemake/snakemake-wrappers/issues/3099)) ([a09832a](https://www.github.com/snakemake/snakemake-wrappers/commit/a09832ae1ada3771d130087bc6dec5656b635643)) * autobump bio/vembrane/filter ([#3111](https://www.github.com/snakemake/snakemake-wrappers/issues/3111)) ([5ec4df5](https://www.github.com/snakemake/snakemake-wrappers/commit/5ec4df572af0fed2589579cd4bc7be8749d55886)) * autobump bio/vembrane/table ([#3112](https://www.github.com/snakemake/snakemake-wrappers/issues/3112)) ([9411cc9](https://www.github.com/snakemake/snakemake-wrappers/commit/9411cc94ed21493c62cc4fcd27307a87fe205e34)) * autobump bio/vep/plugins ([#3113](https://www.github.com/snakemake/snakemake-wrappers/issues/3113)) ([4e7d29b](https://www.github.com/snakemake/snakemake-wrappers/commit/4e7d29b0aba8e20b2df8754d551de81a4c83fb53)) --- This PR was generated with [Release Please](https://github.com/googleapis/release-please). See [documentation](https://github.com/googleapis/release-please#release-please). Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> --- CHANGELOG.md | 24 ++++++++++++++++++++++++ 1 file changed, 24 insertions(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 477b6f9a13f..9b444d7f07e 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -1,5 +1,29 @@ # Changelog +### [3.14.1](https://www.github.com/snakemake/snakemake-wrappers/compare/v3.14.0...v3.14.1) (2024-08-09) + + +### Bug Fixes + +* add missing raw string in REGEX_RULES ([#3104](https://www.github.com/snakemake/snakemake-wrappers/issues/3104)) ([74a3269](https://www.github.com/snakemake/snakemake-wrappers/commit/74a3269fe7152464e8134d7560a32540e4197977)) +* download already indexed vep cache tarball ([#3102](https://www.github.com/snakemake/snakemake-wrappers/issues/3102)) ([13c6ef7](https://www.github.com/snakemake/snakemake-wrappers/commit/13c6ef74db8f6c4608c87f6209bab69b3e9ed16a)) + + +### Performance Improvements + +* autobump bio/encode_fastq_downloader ([#3105](https://www.github.com/snakemake/snakemake-wrappers/issues/3105)) ([695ab1b](https://www.github.com/snakemake/snakemake-wrappers/commit/695ab1b1e39ec2a9693ef5f721bc564e50f716e2)) +* autobump bio/gatk3/indelrealigner ([#3106](https://www.github.com/snakemake/snakemake-wrappers/issues/3106)) ([09d6e0b](https://www.github.com/snakemake/snakemake-wrappers/commit/09d6e0b0d0857c88f6f2c81aec3d7714eb9fb738)) +* autobump bio/gdc-api/bam-slicing ([#3096](https://www.github.com/snakemake/snakemake-wrappers/issues/3096)) ([248b611](https://www.github.com/snakemake/snakemake-wrappers/commit/248b611f33ce879ad40eef4b78ad2d84cda43948)) +* autobump bio/last/lastal ([#3108](https://www.github.com/snakemake/snakemake-wrappers/issues/3108)) ([9f7a264](https://www.github.com/snakemake/snakemake-wrappers/commit/9f7a264c5ceb560008945a4520960e219f470827)) +* autobump bio/last/lastdb ([#3107](https://www.github.com/snakemake/snakemake-wrappers/issues/3107)) ([b1c3334](https://www.github.com/snakemake/snakemake-wrappers/commit/b1c333462d4540a4ed995af2a190bdab0f43e66a)) +* autobump bio/mapdamage2 ([#3109](https://www.github.com/snakemake/snakemake-wrappers/issues/3109)) ([a870b8e](https://www.github.com/snakemake/snakemake-wrappers/commit/a870b8ef9bc89a18b093dc6303048b5e1202f740)) +* autobump bio/sourmash/compute ([#3098](https://www.github.com/snakemake/snakemake-wrappers/issues/3098)) ([5796bc6](https://www.github.com/snakemake/snakemake-wrappers/commit/5796bc6fe0908c4922bb8bfc93183df72afa04b2)) +* autobump bio/spades/metaspades ([#3110](https://www.github.com/snakemake/snakemake-wrappers/issues/3110)) ([e7fb075](https://www.github.com/snakemake/snakemake-wrappers/commit/e7fb075ad006c26c407927f37fe6c0e40b15336e)) +* autobump bio/unicycler ([#3099](https://www.github.com/snakemake/snakemake-wrappers/issues/3099)) ([a09832a](https://www.github.com/snakemake/snakemake-wrappers/commit/a09832ae1ada3771d130087bc6dec5656b635643)) +* autobump bio/vembrane/filter ([#3111](https://www.github.com/snakemake/snakemake-wrappers/issues/3111)) ([5ec4df5](https://www.github.com/snakemake/snakemake-wrappers/commit/5ec4df572af0fed2589579cd4bc7be8749d55886)) +* autobump bio/vembrane/table ([#3112](https://www.github.com/snakemake/snakemake-wrappers/issues/3112)) ([9411cc9](https://www.github.com/snakemake/snakemake-wrappers/commit/9411cc94ed21493c62cc4fcd27307a87fe205e34)) +* autobump bio/vep/plugins ([#3113](https://www.github.com/snakemake/snakemake-wrappers/issues/3113)) ([4e7d29b](https://www.github.com/snakemake/snakemake-wrappers/commit/4e7d29b0aba8e20b2df8754d551de81a4c83fb53)) + ## [3.14.0](https://www.github.com/snakemake/snakemake-wrappers/compare/v3.13.8...v3.14.0) (2024-07-31) From 0c3b69ecbda35b55ca3c9176ceab0df8aea4edc0 Mon Sep 17 00:00:00 2001 From: "snakedeploy-bot[bot]" <115615832+snakedeploy-bot[bot]@users.noreply.github.com> Date: Tue, 13 Aug 2024 07:30:11 +0000 Subject: [PATCH 39/62] perf: autobump bio/cnv_facets (#2775) Automatic bump of bio/cnv_facets. ## Summary by CodeRabbit - **New Features** - Updated the package URL for `cnv_facets` to ensure a consistent reference. - Removed specific Python version dependency in the environment configuration, allowing greater flexibility for users with different Python versions. These changes enhance usability and adaptability within various development environments. --------- Co-authored-by: snakedeploy-bot[bot] <115615832+snakedeploy-bot[bot]@users.noreply.github.com> Co-authored-by: Filipe G. Vieira <1151762+fgvieira@users.noreply.github.com> --- bio/cnv_facets/environment.linux-64.pin.txt | 2 +- bio/cnv_facets/environment.yaml | 1 - 2 files changed, 1 insertion(+), 2 deletions(-) diff --git a/bio/cnv_facets/environment.linux-64.pin.txt b/bio/cnv_facets/environment.linux-64.pin.txt index b9ecbc92047..b0980012d9d 100644 --- a/bio/cnv_facets/environment.linux-64.pin.txt +++ b/bio/cnv_facets/environment.linux-64.pin.txt @@ -169,4 +169,4 @@ https://conda.anaconda.org/conda-forge/noarch/r-waldo-0.2.5-r36hc72bb7e_0.tar.bz https://conda.anaconda.org/conda-forge/linux-64/r-testthat-3.0.2-r36h03ef668_0.tar.bz2#f5b7eee325069aa1a86321fac5a91faf https://conda.anaconda.org/conda-forge/linux-64/r-isoband-0.2.4-r36h03ef668_0.tar.bz2#b32343b8ea36dbc58453d90450210833 https://conda.anaconda.org/conda-forge/noarch/r-ggplot2-3.3.3-r36hc72bb7e_0.tar.bz2#2723ddc160ae13de73d3960cf8cb2492 -https://conda.anaconda.org/bioconda/linux-64/cnv_facets-0.16.0-py38r36h4b26f60_1.tar.bz2#1cf5ad044d30158a6c93089852f200d4 +https://conda.anaconda.org/bioconda/linux-64/cnv_facets-0.16.0-py38r36h4b26f60_1.tar.bz2#1cf5ad044d30158a6c93089852f200d4 \ No newline at end of file diff --git a/bio/cnv_facets/environment.yaml b/bio/cnv_facets/environment.yaml index 7592e0d0fb9..8c9b189d081 100644 --- a/bio/cnv_facets/environment.yaml +++ b/bio/cnv_facets/environment.yaml @@ -4,4 +4,3 @@ channels: - nodefaults dependencies: - cnv_facets =0.16.0 - - python =3.8.15 From a6b078ec3956a65abc7869e2ff21604f79bec20c Mon Sep 17 00:00:00 2001 From: "github-actions[bot]" <41898282+github-actions[bot]@users.noreply.github.com> Date: Tue, 13 Aug 2024 13:02:50 +0200 Subject: [PATCH 40/62] chore: release 3.14.2 (#3114) :robot: I have created a release \*beep\* \*boop\* --- ### [3.14.2](https://www.github.com/snakemake/snakemake-wrappers/compare/v3.14.1...v3.14.2) (2024-08-13) ### Performance Improvements * autobump bio/cnv_facets ([#2775](https://www.github.com/snakemake/snakemake-wrappers/issues/2775)) ([0c3b69e](https://www.github.com/snakemake/snakemake-wrappers/commit/0c3b69ecbda35b55ca3c9176ceab0df8aea4edc0)) --- This PR was generated with [Release Please](https://github.com/googleapis/release-please). See [documentation](https://github.com/googleapis/release-please#release-please). ## Summary by CodeRabbit - **Documentation** - Updated the changelog to include the new version entry for 3.14.2, highlighting performance improvements and enhancements to the `bio/cnv_facets` feature. Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> --- CHANGELOG.md | 7 +++++++ 1 file changed, 7 insertions(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 9b444d7f07e..7c379e6b881 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -1,5 +1,12 @@ # Changelog +### [3.14.2](https://www.github.com/snakemake/snakemake-wrappers/compare/v3.14.1...v3.14.2) (2024-08-13) + + +### Performance Improvements + +* autobump bio/cnv_facets ([#2775](https://www.github.com/snakemake/snakemake-wrappers/issues/2775)) ([0c3b69e](https://www.github.com/snakemake/snakemake-wrappers/commit/0c3b69ecbda35b55ca3c9176ceab0df8aea4edc0)) + ### [3.14.1](https://www.github.com/snakemake/snakemake-wrappers/compare/v3.14.0...v3.14.1) (2024-08-09) From d8ee6cb1d15537cd8a42c38b9f2116cc77fa2880 Mon Sep 17 00:00:00 2001 From: "Filipe G. Vieira" <1151762+fgvieira@users.noreply.github.com> Date: Tue, 13 Aug 2024 13:03:11 +0200 Subject: [PATCH 41/62] feat!: switch to nonpareil utils script for plotting (#3100) ### QC * [x] I confirm that I have followed the [documentation for contributing to `snakemake-wrappers`](https://snakemake-wrappers.readthedocs.io/en/stable/contributing.html). While the contributions guidelines are more extensive, please particularly ensure that: * [x] `test.py` was updated to call any added or updated example rules in a `Snakefile` * [x] `input:` and `output:` file paths in the rules can be chosen arbitrarily * [x] wherever possible, command line arguments are inferred and set automatically (e.g. based on file extensions in `input:` or `output:`) * [x] temporary files are either written to a unique hidden folder in the working directory, or (better) stored where the Python function `tempfile.gettempdir()` points to * [x] the `meta.yaml` contains a link to the documentation of the respective tool or command under `url:` * [x] conda environments use a minimal amount of channels and packages, in recommended ordering --- .../plot/environment.linux-64.pin.txt | 6 +- bio/nonpareil/plot/environment.yaml | 1 - bio/nonpareil/plot/meta.yaml | 18 +- bio/nonpareil/plot/test/Snakefile | 40 +---- bio/nonpareil/plot/wrapper.R | 156 ------------------ bio/nonpareil/plot/wrapper.py | 19 +++ 6 files changed, 33 insertions(+), 207 deletions(-) delete mode 100644 bio/nonpareil/plot/wrapper.R create mode 100644 bio/nonpareil/plot/wrapper.py diff --git a/bio/nonpareil/plot/environment.linux-64.pin.txt b/bio/nonpareil/plot/environment.linux-64.pin.txt index 153ca511610..00ab4365840 100644 --- a/bio/nonpareil/plot/environment.linux-64.pin.txt +++ b/bio/nonpareil/plot/environment.linux-64.pin.txt @@ -81,18 +81,18 @@ https://conda.anaconda.org/conda-forge/linux-64/fontconfig-2.14.2-h14ed4e7_0.con https://conda.anaconda.org/conda-forge/linux-64/gfortran_impl_linux-64-14.1.0-he4a1faa_0.conda#a9ce7cd0848a93a8df88c1fc0ac84d9d https://conda.anaconda.org/conda-forge/linux-64/gxx_impl_linux-64-14.1.0-h2879b86_0.conda#47d6de998d7a285b98b60bce2fecb54b https://conda.anaconda.org/conda-forge/linux-64/libblas-3.9.0-23_linux64_openblas.conda#96c8450a40aa2b9733073a9460de972c -https://conda.anaconda.org/conda-forge/linux-64/libcurl-8.9.0-hdb1bdb2_0.conda#5badfbdb2688d8aaca7bd3c98d557b97 +https://conda.anaconda.org/conda-forge/linux-64/libcurl-8.9.1-hdb1bdb2_0.conda#7da1d242ca3591e174a3c7d82230d3c0 https://conda.anaconda.org/conda-forge/linux-64/xorg-libxext-1.3.4-h0b41bf4_2.conda#82b6df12252e6f32402b96dacc656fec https://conda.anaconda.org/conda-forge/linux-64/xorg-libxrender-0.9.11-hd590300_0.conda#ed67c36f215b310412b2af935bf3e530 https://conda.anaconda.org/conda-forge/linux-64/xorg-libxt-1.3.0-hd590300_1.conda#ae92aab42726eb29d16488924f7312cb https://conda.anaconda.org/conda-forge/linux-64/cairo-1.18.0-hebfffa5_3.conda#fceaedf1cdbcb02df9699a0d9b005292 -https://conda.anaconda.org/conda-forge/linux-64/curl-8.9.0-h18eb788_0.conda#cb385c8a955ad49c3342b23cd1a26c11 +https://conda.anaconda.org/conda-forge/linux-64/curl-8.9.1-h18eb788_0.conda#2e7dedf73dfbfcee662e2a0f6175e4bb https://conda.anaconda.org/conda-forge/linux-64/libcblas-3.9.0-23_linux64_openblas.conda#eede29b40efa878cbe5bdcb767e97310 https://conda.anaconda.org/conda-forge/linux-64/liblapack-3.9.0-23_linux64_openblas.conda#2af0879961951987e464722fd00ec1e0 https://conda.anaconda.org/conda-forge/linux-64/gsl-2.7-he838d99_0.tar.bz2#fec079ba39c9cca093bf4c00001825de https://conda.anaconda.org/conda-forge/linux-64/harfbuzz-9.0.0-hda332d3_1.conda#76b32dcf243444aea9c6b804bcfa40b8 https://conda.anaconda.org/conda-forge/linux-64/pango-1.54.0-h4c5309f_1.conda#7df02e445367703cd87a574046e3a6f0 -https://conda.anaconda.org/conda-forge/linux-64/r-base-4.3.3-h9967228_12.conda#88e0b778762c6ffa75241d0f34cfa94e +https://conda.anaconda.org/conda-forge/linux-64/r-base-4.3.3-h9967228_13.conda#d27cdc47236c6dfeface59c344494495 https://conda.anaconda.org/conda-forge/noarch/r-getopt-1.20.4-r43ha770c72_1.conda#cf6793c369dbc7ef63d9c1bc9b186615 https://conda.anaconda.org/conda-forge/linux-64/r-jsonlite-1.8.8-r43hb1dbf0f_1.conda#eb4377db2a26436aed657474aad972aa https://conda.anaconda.org/conda-forge/noarch/r-optparse-1.7.5-r43hc72bb7e_1.conda#ae32080aac0f74e73e7cd6e774db1c73 diff --git a/bio/nonpareil/plot/environment.yaml b/bio/nonpareil/plot/environment.yaml index e7aec96bc4f..df5fea631cb 100644 --- a/bio/nonpareil/plot/environment.yaml +++ b/bio/nonpareil/plot/environment.yaml @@ -4,4 +4,3 @@ channels: - nodefaults dependencies: - nonpareil =3.5.5 - - r-jsonlite diff --git a/bio/nonpareil/plot/meta.yaml b/bio/nonpareil/plot/meta.yaml index 39da4fc1b1a..d3057e56d50 100644 --- a/bio/nonpareil/plot/meta.yaml +++ b/bio/nonpareil/plot/meta.yaml @@ -4,18 +4,10 @@ url: https://nonpareil.readthedocs.io/en/latest/ authors: - Filipe G. Vieira input: - - NPO file + - NPO file(s) output: - - PDF file with plot + - PDF file with plot (optional) + - TSV file with summary stats (optional) + - JSON file with detailed info (optional) params: - - labels: Curve labels. - - col: Curve colors. - - enforce_consistency: Fails verbosely on insufficient data, otherwise it warns about the inconsistencies and attempts the estimations. - - star: Objective coverage in percentage (i.e., coverage value considered near-complete). - - correction_factor: Apply overlap-dependent correction factor, otherwise redundancy is assumed to equal coverage. - - weights_exp: Vector of values to be tested as exponent of the weights distribution. - - skip_model: Skip model estimation. - - plot_observed: Plot observed values? - - plot_model: Plot infered model? - - plot_dispersion: Plot dispersion around curve (one of `sd`, `ci95`, `ci90`, `ci50`, or `iq`)? - - plot_diversity: Plot diversity (bottom arrow)? + - extra: additional program arguments (not `--pdf`, `--tsv`, or `--json`). diff --git a/bio/nonpareil/plot/test/Snakefile b/bio/nonpareil/plot/test/Snakefile index 86b44e6096a..2ce3defc0b5 100644 --- a/bio/nonpareil/plot/test/Snakefile +++ b/bio/nonpareil/plot/test/Snakefile @@ -3,23 +3,13 @@ rule test_nonpareil_plot: npo="{sample}.npo", output: pdf="results/{sample}.pdf", - model="results/{sample}.RData", + tsv="results/{sample}.tsv", json="results/{sample}.json", threads: 1 log: "logs/{sample}.log", params: - labels=lambda w: w.sample, - col="blue", - enforce_consistency=True, - star=95, - correction_factor=True, - weights_exp=[-1.1,-1.2,-0.9,-1.3,-1], - skip_model=False, - plot_observed=True, - plot_model=True, - plot_dispersion="ci95", - plot_diversity=False, + extra=lambda w: f"--labels {w.sample} --col blue", wrapper: "master/bio/nonpareil/plot" @@ -29,38 +19,20 @@ use rule test_nonpareil_plot as test_nonpareil_plot_multiple with: npo=["a.npo", "b.npo", "c.npo"], output: pdf="results/samples.pdf", - model="results/samples.RData", + tsv="results/samples.tsv", json="results/samples.json", log: "logs/samples.log", params: - labels=["Model A","Model B", "Model C"], - col=["blue","red"], - enforce_consistency=True, - star=95, - correction_factor=True, - plot_observed=True, - plot_model=True, - plot_dispersion="sd", - plot_diversity=True, + extra="--labels 'Model A,Model B,Model C' --col blue,red,green", use rule test_nonpareil_plot as test_nonpareil_plot_nomodel with: output: pdf="results/{sample}.nomodel.pdf", - model="results/{sample}.nomodel.RData", + tsv="results/{sample}.nomodel.tsv", json="results/{sample}.nomodel.json", log: "logs/{sample}.nomodel.log", params: - labels=lambda w: w.sample, - col="blue", - enforce_consistency=True, - star=95, - correction_factor=True, - weights_exp=[-1.1,-1.2,-0.9,-1.3,-1], - skip_model=True, - plot_observed=True, - plot_model=True, - plot_dispersion="iq", - plot_diversity=True + extra=lambda w: f"--labels {w.sample} --col blue --no-model", diff --git a/bio/nonpareil/plot/wrapper.R b/bio/nonpareil/plot/wrapper.R deleted file mode 100644 index 1682f8f76c0..00000000000 --- a/bio/nonpareil/plot/wrapper.R +++ /dev/null @@ -1,156 +0,0 @@ -# __author__ = "Filipe G. Vieira" -# __copyright__ = "Copyright 2023, Filipe G. Vieira" -# __license__ = "MIT" - -# This script plots results (NPO file) from NonPareil - - -# Sink the stderr and stdout to the snakemake log file -# https://stackoverflow.com/a/48173272 -log.file <- file(snakemake@log[[1]], open = "wt") -base::sink(log.file) -base::sink(log.file, type = "message") - - -# Loading libraries (order matters) -base::library(package = "Nonpareil", character.only = TRUE) -base::message("Libraries loaded") - - -# Set input and output files -in_files = snakemake@input[["npo"]] -out_pdf = snakemake@output[[1]] -base::message("Input files: ") -base::print(in_files) - -# Set parameters -params <- list("in_files" = in_files, - "out_pdf" = out_pdf, - "labels" = NA, - "col" = NA, - "enforce_consistency" = ifelse("enforce_consistency" %in% base::names(snakemake@params), as.logical(snakemake@params[["enforce_consistency"]]), FALSE), - "star" = ifelse("star" %in% base::names(snakemake@params), snakemake@params[["star"]], 95), - "correction_factor" = ifelse("correction_factor" %in% base::names(snakemake@params), as.logical(snakemake@params[["correction_factor"]]), FALSE), - "weights_exp" = NA, - "skip_model" = ifelse("skip_model" %in% base::names(snakemake@params), as.logical(snakemake@params[["skip_model"]]), FALSE), - "plot_observed" = ifelse("plot_observed" %in% base::names(snakemake@params), as.logical(snakemake@params[["plot_observed"]]), TRUE), - "plot_model" = ifelse("plot_model" %in% base::names(snakemake@params), as.logical(snakemake@params[["plot_model"]]), TRUE), - "plot_dispersion" = ifelse("plot_dispersion" %in% base::names(snakemake@params), snakemake@params[["plot_dispersion"]], FALSE), - "plot_diversity" = ifelse("plot_diversity" %in% base::names(snakemake@params), as.logical(snakemake@params[["plot_diversity"]]), FALSE) - ) - -# Not sure why, by using "ifelse" only keeps the first element of the vector -if ("labels" %in% base::names(snakemake@params)) { - params[["labels"]] = snakemake@params[["labels"]] - } - -if ("col" %in% base::names(snakemake@params)) { - params[["col"]] = snakemake@params[["col"]] - } - -if ("weights_exp" %in% base::names(snakemake@params)) { - params[["weights_exp"]] = snakemake@params[["weights_exp"]] - } - -base::message("Options provided:") -utils::str(params) - - - -################## -### Save plots ### -################## -pdf(out_pdf) -curves <- Nonpareil.set(in_files, - labels = params[["labels"]], - col = params[["col"]], - enforce.consistency = params[["enforce_consistency"]], - star = params[["star"]], - correction.factor = params[["correction_factor"]], - weights.exp = params[["weights_exp"]], - skip.model = params[["skip_model"]], - plot = FALSE - ) - -lapply(curves$np.curves, plot, - col = params[["col"]], - plot.observed = params[["plot_observed"]], - plot.model = params[["plot_model"]], - plot.dispersion = params[["plot_dispersion"]], - plot.diversity = params[["plot_diversity"]] -) -dev.off() -base::message("Nonpareil plot saved") - - - -################## -### Save stats ### -################## -stats <- summary(curves) -# Fix names -colnames(stats) <- c("Redundancy", "Avg. coverage", "Seq. effort", "Model correlation", "Required seq. effort", "Diversity") -# Print stats to log -base::print(stats) - - - -################## -### Save model ### -################## -if ("model" %in% base::names(snakemake@output)) { - save(curves, file=snakemake@output[["model"]]) -} - - - -################# -### Save JSON ### -################# -if ("json" %in% base::names(snakemake@output)) { - base::library("jsonlite") - base::message("Exporting model as JSON") - - export_curve <- function(object){ - # Extract variables - n <- names(attributes(object))[c(1:12,21:29)] - x <- sapply(n, function(v) attr(object,v)) - names(x) <- n - # Extract vectors - n <- names(attributes(object))[13:20] - y <- lapply(n, function(v) attr(object,v)) - names(y) <- n - curve_json <- c(x, y) - - # Add model - if (object$has.model) { - # https://github.com/lmrodriguezr/nonpareil/blob/162f1697ab1a21128e1857dd87fa93011e30c1ba/utils/Nonpareil/R/Nonpareil.R#L330-L332 - x_min <- 1e3 - x_max <- signif(tail(attr(object,"x.adj"), n=1)*10, 1) - x.model <- exp(seq(log(x_min), log(x_max), length.out=1e3)) - y.model <- predict(object, lr=x.model) - curve_json <- append(curve_json, list(x.model=x.model)) - curve_json <- append(curve_json, list(y.model=y.model)) - } - - base::print(curve_json) - curve_json - } - - export_set <- function(object){ - y <- lapply(object$np.curves, "export_curve") - names(y) <- sapply(object$np.curves, function(n) n$label) - jsonlite::prettify(toJSON(y, auto_unbox=TRUE)) - } - - y <- export_set(curves) - write(y, snakemake@output[["json"]]) - base::message("JSON file saved") -} - - - -# Proper syntax to close the connection for the log file -# but could be optional for Snakemake wrapper -base::sink(type = "message") -base::sink() diff --git a/bio/nonpareil/plot/wrapper.py b/bio/nonpareil/plot/wrapper.py new file mode 100644 index 00000000000..14debb7190f --- /dev/null +++ b/bio/nonpareil/plot/wrapper.py @@ -0,0 +1,19 @@ +__author__ = "Filipe G. Vieira" +__copyright__ = "Copyright 2024, Filipe G. Vieira" +__license__ = "MIT" + + +from pathlib import Path +from snakemake.shell import shell + +extra = snakemake.params.get("extra", "") +log = snakemake.log_fmt_shell(stdout=True, stderr=True) + + +for output in snakemake.output: + ext = Path(output).suffix.lstrip(".") + if ext in ["json", "tsv", "pdf"]: + extra += f" --{ext} {output}" + + +shell("NonpareilCurves.R {extra} {snakemake.input} {log}") From 169a31508f330079799842a21d3b555714365041 Mon Sep 17 00:00:00 2001 From: David Laehnemann Date: Wed, 14 Aug 2024 13:39:48 +0200 Subject: [PATCH 42/62] feat: add ensembl mysql table wrapper (#3103) ### QC * [x] I confirm that I have followed the [documentation for contributing to `snakemake-wrappers`](https://snakemake-wrappers.readthedocs.io/en/stable/contributing.html). While the contributions guidelines are more extensive, please particularly ensure that: * [x] `test.py` was updated to call any added or updated example rules in a `Snakefile` * [x] `input:` and `output:` file paths in the rules can be chosen arbitrarily * [x] wherever possible, command line arguments are inferred and set automatically (e.g. based on file extensions in `input:` or `output:`) * [x] temporary files are either written to a unique hidden folder in the working directory, or (better) stored where the Python function `tempfile.gettempdir()` points to * [x] the `meta.yaml` contains a link to the documentation of the respective tool or command under `url:` * [x] conda environments use a minimal amount of channels and packages, in recommended ordering ## Summary by CodeRabbit - **New Features** - Added a Conda environment setup file for Linux 64-bit systems to simplify package management. - Introduced a specialized Conda environment for bioinformatics projects with key R package dependencies. - Launched a configuration schema to facilitate the creation of biological annotation tables from Ensembl databases. - Implemented new rules in Snakemake for generating repeat and regulatory annotations from Ensembl databases. - Released an R script wrapper for easier interaction with Ensembl databases to retrieve genomic data. - **Bug Fixes** - Enhanced testing coverage with new automated tests for annotation file creation processes. --------- Co-authored-by: Till Hartmann Co-authored-by: coderabbitai[bot] <136622811+coderabbitai[bot]@users.noreply.github.com> --- .../environment.linux-64.pin.txt | 210 ++++++++++++++ .../ensembl-mysql-table/environment.yaml | 9 + bio/reference/ensembl-mysql-table/meta.yaml | 50 ++++ .../ensembl-mysql-table/test/Snakefile | 62 +++++ bio/reference/ensembl-mysql-table/wrapper.R | 258 ++++++++++++++++++ test.py | 30 ++ 6 files changed, 619 insertions(+) create mode 100644 bio/reference/ensembl-mysql-table/environment.linux-64.pin.txt create mode 100644 bio/reference/ensembl-mysql-table/environment.yaml create mode 100644 bio/reference/ensembl-mysql-table/meta.yaml create mode 100644 bio/reference/ensembl-mysql-table/test/Snakefile create mode 100644 bio/reference/ensembl-mysql-table/wrapper.R diff --git a/bio/reference/ensembl-mysql-table/environment.linux-64.pin.txt b/bio/reference/ensembl-mysql-table/environment.linux-64.pin.txt new file mode 100644 index 00000000000..e82b3f7e2ad --- /dev/null +++ b/bio/reference/ensembl-mysql-table/environment.linux-64.pin.txt @@ -0,0 +1,210 @@ +# This file may be used to create an environment using: +# $ conda create --name --file +# platform: linux-64 +@EXPLICIT +https://conda.anaconda.org/conda-forge/linux-64/_libgcc_mutex-0.1-conda_forge.tar.bz2#d7c89558ba9fa0495403155b64376d81 +https://conda.anaconda.org/conda-forge/noarch/_r-mutex-1.0.1-anacondar_1.tar.bz2#19f9db5f4f1b7f5ef5f6d67207f25f38 +https://conda.anaconda.org/conda-forge/noarch/_sysroot_linux-64_curr_repodata_hack-3-h69a702a_16.conda#1c005af0c6ff22814b7c52ee448d4bea +https://conda.anaconda.org/conda-forge/linux-64/ca-certificates-2024.7.4-hbcca054_0.conda#23ab7665c5f63cfb9f1f6195256daac6 +https://conda.anaconda.org/conda-forge/noarch/font-ttf-dejavu-sans-mono-2.37-hab24e00_0.tar.bz2#0c96522c6bdaed4b1566d11387caaf45 +https://conda.anaconda.org/conda-forge/noarch/font-ttf-inconsolata-3.000-h77eed37_0.tar.bz2#34893075a5c9e55cdafac56607368fc6 +https://conda.anaconda.org/conda-forge/noarch/font-ttf-source-code-pro-2.038-h77eed37_0.tar.bz2#4d59c254e01d9cde7957100457e2d5fb +https://conda.anaconda.org/conda-forge/noarch/font-ttf-ubuntu-0.83-h77eed37_2.conda#cbbe59391138ea5ad3658c76912e147f +https://conda.anaconda.org/conda-forge/linux-64/ld_impl_linux-64-2.40-hf3520f5_7.conda#b80f2f396ca2c28b8c14c437a4ed1e74 +https://conda.anaconda.org/conda-forge/noarch/libgcc-devel_linux-64-14.1.0-h5d3d1c9_100.conda#6d4f65dc440f7b3422113b135be19703 +https://conda.anaconda.org/conda-forge/noarch/libstdcxx-devel_linux-64-14.1.0-h5d3d1c9_100.conda#cedc62fd8c4cf28f23d3cd5db7839e99 +https://conda.anaconda.org/conda-forge/linux-64/pandoc-3.2.1-ha770c72_0.conda#b39b12d3809e4042f832b76192e0e7e8 +https://conda.anaconda.org/conda-forge/noarch/tzdata-2024a-h0c530f3_0.conda#161081fc7cec0bfda0d86d7cb595f8d8 +https://conda.anaconda.org/conda-forge/noarch/fonts-conda-forge-1-0.tar.bz2#f766549260d6815b0c52253f1fb1bb29 +https://conda.anaconda.org/conda-forge/noarch/kernel-headers_linux-64-3.10.0-h4a8ded7_16.conda#ff7f38675b226cfb855aebfc32a13e31 +https://conda.anaconda.org/conda-forge/linux-64/libgomp-14.1.0-h77fa898_0.conda#ae061a5ed5f05818acdf9adab72c146d +https://conda.anaconda.org/conda-forge/linux-64/_openmp_mutex-4.5-2_gnu.tar.bz2#73aaf86a425cc6e73fcf236a5a46396d 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a/bio/reference/ensembl-mysql-table/meta.yaml b/bio/reference/ensembl-mysql-table/meta.yaml new file mode 100644 index 00000000000..20a8580a25e --- /dev/null +++ b/bio/reference/ensembl-mysql-table/meta.yaml @@ -0,0 +1,50 @@ +name: ensembl-mysql-table +description: > + Create a table of annotations available via the versioned ensembl mysql databases. + Rows of the resulting table are generated from the mysql database tables specified + under 'main_tables'. If you specify multiple `main_tables`, they should share some + or most of the columns, as they will be stacked on top of each other with + `bind_rows()`. Additional annotation columns beyond those tables can then be given + as mysql tables under 'join_tables'. They have to share a column with all of the + `main_tables`, to allow for `left_join'ing their columns onto them. + The main documentation for the Ensembl mysql databases, including + 'Database schemas', is here: + https://www.ensembl.org/info/docs/api/index.html +url: https://www.ensembl.org/info/docs/api/index.html +authors: + - David Lähnemann +output: + - > + tab-separated values (``.tsv``); for supported compression extensions, see + `the write_tsv documentation page `_ + - > + parquet (``.parquet``) file; for supported compression algorithms, see + `the write_parquet documentation page `_ +params: + - species: > + Species that is available via the Ensembl mysql databases. For a quick + check, see the + `Ensembl species list `_. + For full valid species names, consult the respective table for the + `release` you specify, for example for '112' this is at: + https://ftp.ensembl.org/pub/release-112/species_EnsemblVertebrates.txt + - build: build available for the selected species, for example 'GRCh38' + - release: release from which the species and build are available, for example '112' + - main_tables: > + A list of wanted ``main_tables``. You have to specify them as a dictionary in the + format ``{ table_name : database }``. You can find available tables in the + ``Database schema``s in the Ensembl documentation: + https://mart.ensembl.org/info/docs/api/index.html + Available ``database`` names at the time of writing are ``core``, ``cdna``, + ``funcgen``, ``compara``, ``rnaseq``, ``variation``, ``otherfeatures``. + You can also interactively explore the available databases and tables, for + example following this walkthrough: + https://tavareshugo.github.io/data_carpentry_extras/dbplyr_ensembl/dbplyr_ensembl.html + - join_tables: > + (optional) A list of ``join_tables`` to add further annotation columns. You have + to specify them as a nested dictionary in the format: + ``{ table_name : { "database": database, "join_column": join_column_name } }`` + As for ``main_tables``, most info can be found in the ``Database schema``s: + https://mart.ensembl.org/info/docs/api/index.html + And for more detailed infos, you'll have to interactively explore the mysql databases: + https://tavareshugo.github.io/data_carpentry_extras/dbplyr_ensembl/dbplyr_ensembl.html diff --git a/bio/reference/ensembl-mysql-table/test/Snakefile b/bio/reference/ensembl-mysql-table/test/Snakefile new file mode 100644 index 00000000000..e2e4033caee --- /dev/null +++ b/bio/reference/ensembl-mysql-table/test/Snakefile @@ -0,0 +1,62 @@ +rule create_repeat_annotations: + output: + table="resources/ensembl_repeat_annotations.tsv.gz", # .gz extension is optional, but recommended + params: + species="homo_sapiens", + build="GRCh37", + release="105", + main_tables={ + "repeat_feature": { + "database": "core", + }, + }, # choose the main table to retrieve, specifying { table : database } + join_tables={ + "seq_region": { + "database": "core", + "join_column": "seq_region_id", + }, + "repeat_consensus": { + "database": "core", + "join_column": "repeat_consensus_id", + }, + }, + # optional: add tables to join in for further annotations, specifying { table : { "database": database, "join_column": join-column } } + log: + "logs/create_repeat_annotations.log", + cache: "omit-software" # save space and time with between workflow caching (see docs) + wrapper: + "master/bio/reference/ensembl-mysql-table" + + +rule create_regulatory_annotations_parquet: + output: + table="resources/ensembl_regulatory_annotations.parquet.gz", # .gz extension is optional, but recommended + params: + species="mus_musculus", + build="GRCm39", + release="112", + main_tables={ + "regulatory_feature": { + "database": "funcgen", + }, + "mirna_target_feature": { + "database": "funcgen", + }, + }, + # choose the main table to retrieve, specifying { table : database } + join_tables={ + "seq_region": { + "database": "core", + "join_column": "seq_region_id" + }, + "feature_type": { + "database": "funcgen", + "join_column": "feature_type_id" + }, + }, + # optional: add tables to join in for further annotations, specifying { table : { "database": database, "join_column": join-column } } + log: + "logs/create_regulatory_annotations_parquet.log", + cache: "omit-software" # save space and time with between workflow caching (see docs) + wrapper: + "master/bio/reference/ensembl-mysql-table" diff --git a/bio/reference/ensembl-mysql-table/wrapper.R b/bio/reference/ensembl-mysql-table/wrapper.R new file mode 100644 index 00000000000..a4b6e75c973 --- /dev/null +++ b/bio/reference/ensembl-mysql-table/wrapper.R @@ -0,0 +1,258 @@ +# __author__ = "David Lähnemann" +# __copyright__ = "Copyright 2024, David Lähnemann" +# __email__ = "david.laehnemann@hhu.de" +# __license__ = "MIT" + +log <- file(snakemake@log[[1]], open="wt") +sink(log) +sink(log, type="message") + +library("tidyverse") +library("nanoparquet") +rlang::global_entrace() +library("fs") +library("cli") + +library("dbplyr") +library("RMariaDB") + +wanted_species <- snakemake@params[["species"]] +wanted_release <- snakemake@params[["release"]] +wanted_build <- snakemake@params[["build"]] + +main_tables <- snakemake@params[["main_tables"]] +join_tables <- snakemake@params[["join_tables"]] + +output_filename <- snakemake@output[["table"]] + +if (wanted_build == "GRCh37") { + port <- 3337 +} else if (wanted_build == "GRCm38") { + if (wanted_release > 99) { + cli_abort(c( + "From Ensembl release 100 and upwards, genome build GRCm38 is not available any more.", + "i" = "Please choose a release of 99 or lower, or choose a newer mouse genome build.", + )) + } + port <- 3337 +} else { + port <- 3306 +} + +# general connection to ensembl databases +ensembl_connection <- dbConnect( + MariaDB(), + host = "ensembldb.ensembl.org", + user = "anonymous", + port = port, + password = "", + timeout=45 +) + +get_and_check_db_name <- function(connection, species, database, release, wanted_build) { + species_dbs <- dbGetQuery(connection, "SHOW DATABASES") |> filter(str_starts(Database, species)) + + dbname_prefix <- str_c( + species, + database, + release, + sep ="_" + ) + dbname <- species_dbs |> filter(str_starts(Database, dbname_prefix)) |> pull(Database) + + core_dbname_prefix <- str_c( + species, + "core", + release, + sep ="_" + ) + core_dbname <- species_dbs |> filter(str_starts(Database, core_dbname_prefix)) |> pull(Database) + + if ( length(dbname) == 1 ) { + # CHECK THAT WE ARE GETTING THE CORRECT BUILD + # 1st option: the meta table of the core database contains build / assembly + # identifiers that match what is requested + core_connection <- dbConnect( + MariaDB(), + dbname = core_dbname, + host = "ensembldb.ensembl.org", + user = "anonymous", + port = port, + password = "", + timeout=45 + ) + assembly_default <- tbl(core_connection, "meta") |> filter(meta_key == "assembly.default") |> pull("meta_value") + assembly_name <- tbl(core_connection, "meta") |> filter(meta_key == "assembly.name") |> pull("meta_value") + + if (!wanted_build %in% c(assembly_default, assembly_name)) { + # 2nd option: the build number from the retrieved database name matches + # the systematically parsed version number at the end of + # the build requested via params: + + retrieved_build_num <- dbname |> first() |> str_split("_") |> first() |> last() + + # Canonicalize the build number to a single number as used in the mysql + # database names. At the time of writing, this code fails for 20 species, + # but build/assembly name numbers in those have no systematic relationship + # with the build numbers used in the respective mysql databases. Thus, we + # throw an error in those cases and ask users to check up the correct + # matchup manually. + wanted_build_num <- wanted_build |> + # remove patch suffixes like ".p14" in "GRCh38.p14", although usually + # we expect users of the wrapper to only specify "GRCh38" as the build + str_replace("\\.p\\d+$", "") |> + # look for trailing combinations of digits and dots + str_extract("[\\d\\.]+$") |> + # remove all dots, as mysql database numbers contain no dots + str_replace_all( "\\.", "") |> + # remove leading zeros, for example from "PKINGS_0.1" + str_replace( "^0+", "") |> + # remove trailing zeros, as this is needed for the vast majority of such + # cases (but in some cases this causes a mismatch, but there is no + # systematic way of resolving when) + str_replace("0$", "") + + if (retrieved_build_num != wanted_build_num) { + # 3rd option: try matching up by downloading the releases species + # summary file from the FTP servers... ¯\_(ツ)_/¯ + species_file_address <- str_c( + "https://ftp.ensembl.org/pub/release-", + release, + "/species_EnsemblVertebrates.txt" + ) + species_summary <- read_tsv(species_file_address) |> + filter( str_starts(core_db, species) ) |> + select(assembly, core_db) + assembly <- species_summary |> pull(assembly) |> first() + summary_build_num <- species_summary |> pull(core_db) |> first() |> str_split("_") |> first() |> last() + if ( (! str_starts(wanted_build, assembly)) & (summary_build_num != wanted_build_num) ) { + cli_abort(c( + "The build we could retrieve for the specified combination of species, database, and release does", + "not match the build you specified.", + "x" = "You specified:", + "*" = "genome build: {wanted_build}", + "*" = "species: {species}", + "*" = "Ensembl release {release}", + "x" = "But the 'meta' table of the respective 'core' database ('{core_dbname}') gave:", + "*" = "assembly.default: {assembly_default}", + "*" = "assembly.name: {assembly_name}", + " " = "Neither matches the requested genome build.", + " " = "", + "x" = "Also, build number '{retrieved_build_num}' at the end of the determined database name", + " " = "does not match the build number we systematically extracted from '{wanted_build}',", + " " = "which is '{wanted_build_num}'.", + " " = "", + "x" = "Finally, we also checked against the Ensembl species summary file at:", + " " = "{species_file_address}", + " " = "It listed the following info, which doesn't match the wanted build specification:", + "*" = "build / assembly : '{assembly}'", + "*" = "build number for core_db: '{summary_build_num}'", + " " = "We give up.", + " " = "", + "i" = "Please ensure that you specify an existing combination of species, build and release.", + " " = "The Ensembl species summary file for the release you want, is a good starting point.", + " " = " It includes correct 'species' names and valid 'assembly' (build) names:", + " " = "{species_file_address}", + " " = "" + )) + } + } + } + dbname + } else { + cli_abort(c( + "Could not retrieve a (unique?) database name for the specified combination of species, database, release, and build.", + "x" = "You requested", + "*" = "species: {species}", + "*" = "database: {database}", + "*" = "Ensembl release: {release}", + "*" = "genome build: {wanted_build}", + " " = "", + " " = "As builds are simple numbers in the mysql database names, we looked for a database with prefix:", + " " = "{dbname_prefix}", + " " = "", + "x" = "Here's what we found (can be empty):", + " " = "{dbname}", + " " = "", + "i" = "Please ensure that you specify an existing and unique combination of species, database, release, and build.", + " " = "The following species summary file can be a good starting point:", + " " = "https://ftp.ensembl.org/pub/release-{release}/species_EnsemblVertebrates.txt" + )) + } +} + +get_table <- function(dbname, port, table_name) { + table_connection <- dbConnect( + MariaDB(), + dbname = dbname, + host = "ensembldb.ensembl.org", + user = "anonymous", + port = port, + password = "", + timeout=45 + ) + # TODO: This is where we could do filtering, to reduce the amount of actual + # downloading at the earliest possible point. But this would need extra + # params-based syntax, but I'm not sure whether that's really necessary, or + # if most use cases will be about dumping (and joining) full tables. + table <- tbl(table_connection, table_name) |> collect() + table +} + +main_table <- tibble() +for (table in names(main_tables)) { + main_table_db_name <- get_and_check_db_name(ensembl_connection, wanted_species, main_tables[[table]][["database"]], wanted_release, wanted_build) + main_table <- main_table |> + bind_rows( + get_table(main_table_db_name, port, table) + ) +} + +if ( !is.null(join_tables) ) { + for (table in names(join_tables)) { + table_db_name <- get_and_check_db_name(ensembl_connection, wanted_species, join_tables[[table]][["database"]], wanted_release, wanted_build) + tbl <- get_table(table_db_name, port, table) + main_table <- main_table |> + left_join( + tbl, + by = join_tables[[table]][["join_column"]] + ) + } +} + +if ( str_detect(output_filename, "tsv(\\.(gz|bz2|xz))?$") ) { + write_tsv( + x = main_table, + file = output_filename + ) +} else if ( str_detect(output_filename, "\\.parquet") ) { + last_ext <- path_ext(output_filename) + compression <- case_match( + last_ext, + "parquet" ~ "uncompressed", + "gz" ~ "gzip", + "zst" ~ "zstd", + "sz" ~ "snappy" + ) + if ( is.na(compression) ) { + cli_abort( + "File extension '{last_ext}' not supported for writing with the used nanoparquet version.", + "x" = "Cannot write to a file '{output_filename}', because the version of the package", + "nanoparquet used does not support writing files of type '{last_ext}'.", + "i" = "For supported file types, see: https://r-lib.github.io/nanoparquet/reference/write_parquet.html" + ) + } + write_parquet( + x = main_table, + file = output_filename, + compression = compression + ) +} else { + cli_abort(c( + "Unsupported file format in output file '{output_filename}'.", + "x" = "Only '.tsv' and '.parquet' files are supported, with certain compression variants each.", + "i" = "For supported compression extensions, see:", + "*" = "tsv: https://readr.tidyverse.org/reference/write_delim.html#output", + "*" = "parquet: https://r-lib.github.io/nanoparquet/reference/write_parquet.html#arguments" + )) +} diff --git a/test.py b/test.py index cbf1f32e83c..595a665609e 100644 --- a/test.py +++ b/test.py @@ -5673,6 +5673,36 @@ def test_ensembl_transcripts_to_genes_mapping_parquet(): ) +@skip_if_not_modified +def test_ensembl_mysql_create_repeat_annotations(): + run( + "bio/reference/ensembl-mysql-table", + [ + "snakemake", + "--cores", + "1", + "resources/ensembl_repeat_annotations.tsv.gz", + "--use-conda", + "-F", + ], + ) + + +@skip_if_not_modified +def test_ensembl_mysql_create_regulatory_annotations_parquet(): + run( + "bio/reference/ensembl-mysql-table", + [ + "snakemake", + "--cores", + "1", + "resources/ensembl_regulatory_annotations.parquet.gz", + "--use-conda", + "-F", + ], + ) + + @skip_if_not_modified def test_ensembl_variation(): run( From 8b42097598b779ac1de130aca4aa185d33424d33 Mon Sep 17 00:00:00 2001 From: "github-actions[bot]" <41898282+github-actions[bot]@users.noreply.github.com> Date: Wed, 14 Aug 2024 17:22:07 +0200 Subject: [PATCH 43/62] chore: release 4.0.0 (#3115) MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit :robot: I have created a release \*beep\* \*boop\* --- ## [4.0.0](https://www.github.com/snakemake/snakemake-wrappers/compare/v3.14.2...v4.0.0) (2024-08-14) ### ⚠ BREAKING CHANGES * switch to nonpareil utils script for plotting (#3100) ### Features * add ensembl mysql table wrapper ([#3103](https://www.github.com/snakemake/snakemake-wrappers/issues/3103)) ([169a315](https://www.github.com/snakemake/snakemake-wrappers/commit/169a31508f330079799842a21d3b555714365041)) * switch to nonpareil utils script for plotting ([#3100](https://www.github.com/snakemake/snakemake-wrappers/issues/3100)) ([d8ee6cb](https://www.github.com/snakemake/snakemake-wrappers/commit/d8ee6cb1d15537cd8a42c38b9f2116cc77fa2880)) --- This PR was generated with [Release Please](https://github.com/googleapis/release-please). See [documentation](https://github.com/googleapis/release-please#release-please). Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> --- CHANGELOG.md | 12 ++++++++++++ 1 file changed, 12 insertions(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 7c379e6b881..0279434bd9e 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -1,5 +1,17 @@ # Changelog +## [4.0.0](https://www.github.com/snakemake/snakemake-wrappers/compare/v3.14.2...v4.0.0) (2024-08-14) + + +### ⚠ BREAKING CHANGES + +* switch to nonpareil utils script for plotting (#3100) + +### Features + +* add ensembl mysql table wrapper ([#3103](https://www.github.com/snakemake/snakemake-wrappers/issues/3103)) ([169a315](https://www.github.com/snakemake/snakemake-wrappers/commit/169a31508f330079799842a21d3b555714365041)) +* switch to nonpareil utils script for plotting ([#3100](https://www.github.com/snakemake/snakemake-wrappers/issues/3100)) ([d8ee6cb](https://www.github.com/snakemake/snakemake-wrappers/commit/d8ee6cb1d15537cd8a42c38b9f2116cc77fa2880)) + ### [3.14.2](https://www.github.com/snakemake/snakemake-wrappers/compare/v3.14.1...v3.14.2) (2024-08-13) From 6f46508aa99663930e70c82114205929aee2dfcb Mon Sep 17 00:00:00 2001 From: Vito Zanotelli Date: Thu, 15 Aug 2024 09:37:27 +0200 Subject: [PATCH 44/62] fix: Correctly handle non str index list for bwa-mem2/mem (#3101) As reported in #522, currently the `bwa2-mem` wrapper has issues if `idx` is a sequence is it incorrectly checked `input.index` to be as string instead of `input.idx`. This bug was silent, as usually `snakemake.input.index` would always be a available as `functools.partial(, _name='index')` or similar. Thus the predicate that it was not a `str` was always true. Now with `snakemake=8.16.0` this changed and the bug becomes an error running the already existing tests. While the discussion in #522 indicates, that there is an underlying issue with the concept of `input.idx` being as sequence of indices, this may need rework later. Until all the details are decided, having a correct working version should be still valuable. With the current state any workflow using this wrapper using `snakemake=8.16.0` is broken. ### QC * [x] I confirm that I have followed the [documentation for contributing to `snakemake-wrappers`](https://snakemake-wrappers.readthedocs.io/en/stable/contributing.html). While the contributions guidelines are more extensive, please particularly ensure that: * [x] `test.py` was updated to call any added or updated example rules in a `Snakefile` * [x] `input:` and `output:` file paths in the rules can be chosen arbitrarily * [x] wherever possible, command line arguments are inferred and set automatically (e.g. based on file extensions in `input:` or `output:`) * [x] temporary files are either written to a unique hidden folder in the working directory, or (better) stored where the Python function `tempfile.gettempdir()` points to * [x] the `meta.yaml` contains a link to the documentation of the respective tool or command under `url:` * [x] conda environments use a minimal amount of channels and packages, in recommended ordering ## Summary by CodeRabbit - **New Features** - Enhanced documentation clarifying input requirements for index files, ensuring users know all necessary file extensions. - Added a new function to extract the longest common prefix from index file names, improving error handling. - **Bug Fixes** - Updated index file specifications to require a complete list of index files, preventing execution errors due to missing files. - **Documentation** - Improved comments and descriptions in the Snakefile and meta.yaml for better user guidance on index file usage. --------- Co-authored-by: Vito Zanotelli --- bio/bwa-mem2/mem/meta.yaml | 5 ++++- bio/bwa-mem2/mem/test/Snakefile | 8 ++++---- bio/bwa-mem2/mem/test/Snakefile_picard | 4 ++-- bio/bwa-mem2/mem/test/Snakefile_samtools | 4 ++-- bio/bwa-mem2/mem/wrapper.py | 23 ++++++++++++++++++----- 5 files changed, 30 insertions(+), 14 deletions(-) diff --git a/bio/bwa-mem2/mem/meta.yaml b/bio/bwa-mem2/mem/meta.yaml index 4beaa010ffb..ca9d0f67608 100644 --- a/bio/bwa-mem2/mem/meta.yaml +++ b/bio/bwa-mem2/mem/meta.yaml @@ -8,7 +8,10 @@ authors: - Thibault Dayris input: - reads: List of path(s) to FASTQ file(s) - - idx: List of paths to indexed reference genome files + - idx: | + List of paths to indexed reference genome files. + All index files required need to be declared: + ".0123", ".amb", ".ann", ".bwt.2bit.64", ".pac" output: - SAM/BAM/CRAM file notes: | diff --git a/bio/bwa-mem2/mem/test/Snakefile b/bio/bwa-mem2/mem/test/Snakefile index 3c6e779befa..027094c1307 100644 --- a/bio/bwa-mem2/mem/test/Snakefile +++ b/bio/bwa-mem2/mem/test/Snakefile @@ -1,8 +1,8 @@ rule bwa_mem2_mem: input: reads=["reads/{sample}.1.fastq", "reads/{sample}.2.fastq"], - # Index can be a list of (all) files created by bwa, or one of them - idx=multiext("genome.fasta", ".amb", ".ann", ".bwt.2bit.64", ".pac"), + # Index needs to be a list of all index files created by bwa + idx=multiext("genome.fasta", ".amb", ".ann", ".bwt.2bit.64", ".pac", ".0123"), output: "mapped/{sample}.bam", log: @@ -20,8 +20,8 @@ rule bwa_mem2_mem: rule bwa_mem2_mem_sam: input: reads=["reads/{sample}.1.fastq", "reads/{sample}.2.fastq"], - # Index can be a list of (all) files created by bwa, or one of them - idx=multiext("genome.fasta", ".amb", ".ann", ".bwt.2bit.64", ".pac"), + # Index needs to be a list of all index files created by bwa + idx=multiext("genome.fasta", ".amb", ".ann", ".bwt.2bit.64", ".pac", ".0123"), output: "mapped/{sample}.sam", log: diff --git a/bio/bwa-mem2/mem/test/Snakefile_picard b/bio/bwa-mem2/mem/test/Snakefile_picard index dfdba92a9d6..a0c03e0b4a8 100644 --- a/bio/bwa-mem2/mem/test/Snakefile_picard +++ b/bio/bwa-mem2/mem/test/Snakefile_picard @@ -1,8 +1,8 @@ rule bwa_mem2_mem: input: reads=["reads/{sample}.1.fastq", "reads/{sample}.2.fastq"], - # Index can be a list of (all) files created by bwa, or one of them - idx=multiext("genome.fasta", ".amb", ".ann", ".bwt.2bit.64", ".pac"), + # Index needs to be a list of all index files created by bwa + idx=multiext("genome.fasta", ".amb", ".ann", ".bwt.2bit.64", ".pac", ".0123"), output: "mapped/{sample}.bam", log: diff --git a/bio/bwa-mem2/mem/test/Snakefile_samtools b/bio/bwa-mem2/mem/test/Snakefile_samtools index 426c92ab9cf..4c0c490210a 100644 --- a/bio/bwa-mem2/mem/test/Snakefile_samtools +++ b/bio/bwa-mem2/mem/test/Snakefile_samtools @@ -1,8 +1,8 @@ rule bwa_mem2_mem: input: reads=["reads/{sample}.1.fastq", "reads/{sample}.2.fastq"], - # Index can be a list of (all) files created by bwa, or one of them - idx=multiext("genome.fasta", ".amb", ".ann", ".bwt.2bit.64", ".pac"), + # Index needs to be a list of all index files created by bwa + idx=multiext("genome.fasta", ".amb", ".ann", ".bwt.2bit.64", ".pac", ".0123"), output: "mapped/{sample}.bam", log: diff --git a/bio/bwa-mem2/mem/wrapper.py b/bio/bwa-mem2/mem/wrapper.py index f5185fcefc0..28cab1aa828 100644 --- a/bio/bwa-mem2/mem/wrapper.py +++ b/bio/bwa-mem2/mem/wrapper.py @@ -12,6 +12,9 @@ from snakemake_wrapper_utils.java import get_java_opts from snakemake_wrapper_utils.samtools import get_samtools_opts +# All idx required by bwa-mem2 +REQUIRED_IDX = {".0123", ".amb", ".ann", ".bwt.2bit.64", ".pac"} + # Extract arguments. extra = snakemake.params.get("extra", "") @@ -27,11 +30,21 @@ bwa_threads = snakemake.threads samtools_threads = snakemake.threads - 1 -index = snakemake.input.get("index", "") -if isinstance(index, str): - index = path.splitext(snakemake.input.idx)[0] -else: - index = path.splitext(snakemake.input.idx[0])[0] + +# Extract index from input +# and check that all required indices are declared +index = path.commonprefix(snakemake.input.idx)[:-1] + +if len(index) == 0: + raise ValueError("Could not determine common prefix of inputs.idx files.") + +index_extensions = [idx[len(index) :] for idx in snakemake.input.idx] +missing_idx = REQUIRED_IDX - set(index_extensions) +if len(missing_idx) > 0: + raise ValueError( + f"Missing required indices: {missing_idx} declarad as input.idx.\n" + f"Identified reference file is {index} with extensions {index_extensions}" + ) # Check inputs/arguments. From 62922298404397c7b23dc5b8fb01bc33e445e97f Mon Sep 17 00:00:00 2001 From: "snakedeploy-bot[bot]" <115615832+snakedeploy-bot[bot]@users.noreply.github.com> Date: Fri, 16 Aug 2024 02:57:23 +0000 Subject: [PATCH 45/62] perf: autobump bio/genomescope (#3117) Automatic bump of bio/genomescope. --------- Co-authored-by: snakedeploy-bot[bot] <115615832+snakedeploy-bot[bot]@users.noreply.github.com> --- bio/genomescope/environment.linux-64.pin.txt | 136 +++++++++---------- bio/genomescope/environment.yaml | 2 +- 2 files changed, 69 insertions(+), 69 deletions(-) diff --git a/bio/genomescope/environment.linux-64.pin.txt b/bio/genomescope/environment.linux-64.pin.txt index 135c80a4c13..f43ff64d0d6 100644 --- a/bio/genomescope/environment.linux-64.pin.txt +++ b/bio/genomescope/environment.linux-64.pin.txt @@ -4,48 +4,44 @@ @EXPLICIT https://conda.anaconda.org/conda-forge/linux-64/_libgcc_mutex-0.1-conda_forge.tar.bz2#d7c89558ba9fa0495403155b64376d81 https://conda.anaconda.org/conda-forge/noarch/_r-mutex-1.0.1-anacondar_1.tar.bz2#19f9db5f4f1b7f5ef5f6d67207f25f38 -https://conda.anaconda.org/conda-forge/linux-64/ca-certificates-2023.7.22-hbcca054_0.conda#a73ecd2988327ad4c8f2c331482917f2 +https://conda.anaconda.org/conda-forge/noarch/_sysroot_linux-64_curr_repodata_hack-3-h69a702a_16.conda#1c005af0c6ff22814b7c52ee448d4bea +https://conda.anaconda.org/conda-forge/linux-64/ca-certificates-2024.7.4-hbcca054_0.conda#23ab7665c5f63cfb9f1f6195256daac6 https://conda.anaconda.org/conda-forge/noarch/font-ttf-dejavu-sans-mono-2.37-hab24e00_0.tar.bz2#0c96522c6bdaed4b1566d11387caaf45 https://conda.anaconda.org/conda-forge/noarch/font-ttf-inconsolata-3.000-h77eed37_0.tar.bz2#34893075a5c9e55cdafac56607368fc6 https://conda.anaconda.org/conda-forge/noarch/font-ttf-source-code-pro-2.038-h77eed37_0.tar.bz2#4d59c254e01d9cde7957100457e2d5fb 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+https://conda.anaconda.org/bioconda/noarch/genomescope2-2.0.1-py312r43hdfd78af_0.tar.bz2#82032b408db990c84b15aaf56f466227 diff --git a/bio/genomescope/environment.yaml b/bio/genomescope/environment.yaml index e71c5acecf4..2093b8f58e9 100644 --- a/bio/genomescope/environment.yaml +++ b/bio/genomescope/environment.yaml @@ -3,4 +3,4 @@ channels: - bioconda - nodefaults dependencies: - - genomescope2 =2.0 + - genomescope2 =2.0.1 From ba219e7698eb078fe22c703a9662c8cb6deee0eb Mon Sep 17 00:00:00 2001 From: "snakedeploy-bot[bot]" <115615832+snakedeploy-bot[bot]@users.noreply.github.com> Date: Fri, 16 Aug 2024 02:59:24 +0000 Subject: [PATCH 46/62] perf: autobump bio/gatk3/realignertargetcreator (#3118) Automatic bump of bio/gatk3/realignertargetcreator. ## Summary by CodeRabbit - **New Features** - Updated various packages and libraries in the conda environment to newer versions, enhancing overall performance and stability. - Incremented Python version from 3.12.4 to 3.12.5 for improved compatibility and security. - **Bug Fixes** - Upgraded OpenJDK, bzip2, c-ares, libdeflate, openssl, and R packages, which may include bug fixes and optimizations. --------- Co-authored-by: snakedeploy-bot[bot] <115615832+snakedeploy-bot[bot]@users.noreply.github.com> --- .../environment.linux-64.pin.txt | 122 +++++++++--------- .../realignertargetcreator/environment.yaml | 2 +- 2 files changed, 62 insertions(+), 62 deletions(-) diff --git a/bio/gatk3/realignertargetcreator/environment.linux-64.pin.txt b/bio/gatk3/realignertargetcreator/environment.linux-64.pin.txt index 2559e64a564..0bc3b49c587 100644 --- a/bio/gatk3/realignertargetcreator/environment.linux-64.pin.txt +++ b/bio/gatk3/realignertargetcreator/environment.linux-64.pin.txt @@ -13,7 +13,7 @@ https://conda.anaconda.org/conda-forge/noarch/font-ttf-ubuntu-0.83-h77eed37_2.co https://conda.anaconda.org/conda-forge/linux-64/ld_impl_linux-64-2.40-hf3520f5_7.conda#b80f2f396ca2c28b8c14c437a4ed1e74 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(#3119) Automatic bump of bio/gatk3/baserecalibrator. --------- Co-authored-by: snakedeploy-bot[bot] <115615832+snakedeploy-bot[bot]@users.noreply.github.com> --- .../environment.linux-64.pin.txt | 122 +++++++++--------- bio/gatk3/baserecalibrator/environment.yaml | 2 +- 2 files changed, 62 insertions(+), 62 deletions(-) diff --git a/bio/gatk3/baserecalibrator/environment.linux-64.pin.txt b/bio/gatk3/baserecalibrator/environment.linux-64.pin.txt index 2559e64a564..0bc3b49c587 100644 --- a/bio/gatk3/baserecalibrator/environment.linux-64.pin.txt +++ b/bio/gatk3/baserecalibrator/environment.linux-64.pin.txt @@ -13,7 +13,7 @@ https://conda.anaconda.org/conda-forge/noarch/font-ttf-ubuntu-0.83-h77eed37_2.co https://conda.anaconda.org/conda-forge/linux-64/ld_impl_linux-64-2.40-hf3520f5_7.conda#b80f2f396ca2c28b8c14c437a4ed1e74 https://conda.anaconda.org/conda-forge/noarch/libgcc-devel_linux-64-14.1.0-h5d3d1c9_100.conda#6d4f65dc440f7b3422113b135be19703 https://conda.anaconda.org/conda-forge/noarch/libstdcxx-devel_linux-64-14.1.0-h5d3d1c9_100.conda#cedc62fd8c4cf28f23d3cd5db7839e99 -https://conda.anaconda.org/conda-forge/linux-64/openjdk-8.0.412-hd590300_0.conda#7628220319162f8a7b27f8938a0fc484 +https://conda.anaconda.org/conda-forge/linux-64/openjdk-8.0.412-hd590300_1.conda#d2a3445233d7c7b1c739eb088c6703cf https://conda.anaconda.org/conda-forge/noarch/tzdata-2024a-h0c530f3_0.conda#161081fc7cec0bfda0d86d7cb595f8d8 https://conda.anaconda.org/conda-forge/noarch/fonts-conda-forge-1-0.tar.bz2#f766549260d6815b0c52253f1fb1bb29 https://conda.anaconda.org/conda-forge/noarch/kernel-headers_linux-64-3.10.0-h4a8ded7_16.conda#ff7f38675b226cfb855aebfc32a13e31 @@ -23,11 +23,11 @@ https://conda.anaconda.org/conda-forge/noarch/fonts-conda-ecosystem-1-0.tar.bz2# https://conda.anaconda.org/conda-forge/noarch/sysroot_linux-64-2.17-h4a8ded7_16.conda#223fe8a3ff6d5e78484a9d58eb34d055 https://conda.anaconda.org/conda-forge/linux-64/binutils_impl_linux-64-2.40-ha1999f0_7.conda#3f840c7ed70a96b5ebde8044b2f36f32 https://conda.anaconda.org/conda-forge/linux-64/libgcc-ng-14.1.0-h77fa898_0.conda#ca0fad6a41ddaef54a153b78eccb5037 -https://conda.anaconda.org/conda-forge/linux-64/bzip2-1.0.8-hd590300_5.conda#69b8b6202a07720f448be700e300ccf4 -https://conda.anaconda.org/conda-forge/linux-64/c-ares-1.32.0-h4ab18f5_0.conda#7f3a7d68b591fcace97c29c6af6d9d64 +https://conda.anaconda.org/conda-forge/linux-64/bzip2-1.0.8-h4bc722e_7.conda#62ee74e96c5ebb0af99386de58cf9553 +https://conda.anaconda.org/conda-forge/linux-64/c-ares-1.33.0-ha66036c_0.conda#b6927f788e85267beef6cbb292aaebdd https://conda.anaconda.org/conda-forge/linux-64/fribidi-1.0.10-h36c2ea0_0.tar.bz2#ac7bc6a654f8f41b352b38f4051135f8 https://conda.anaconda.org/conda-forge/linux-64/keyutils-1.6.1-h166bdaf_0.tar.bz2#30186d27e2c9fa62b45fb1476b7200e3 -https://conda.anaconda.org/conda-forge/linux-64/libdeflate-1.20-hd590300_0.conda#8e88f9389f1165d7c0936fe40d9a9a79 +https://conda.anaconda.org/conda-forge/linux-64/libdeflate-1.21-h4bc722e_0.conda#36ce76665bf67f5aac36be7a0d21b7f3 https://conda.anaconda.org/conda-forge/linux-64/libev-4.33-hd590300_2.conda#172bf1cd1ff8629f2b1179945ed45055 https://conda.anaconda.org/conda-forge/linux-64/libexpat-2.6.2-h59595ed_0.conda#e7ba12deb7020dd080c6c70e7b6f6a3d https://conda.anaconda.org/conda-forge/linux-64/libffi-3.4.2-h7f98852_5.tar.bz2#d645c6d2ac96843a2bfaccd2d62b3ac3 @@ -42,7 +42,7 @@ https://conda.anaconda.org/conda-forge/linux-64/libxcrypt-4.4.36-hd590300_1.cond https://conda.anaconda.org/conda-forge/linux-64/libzlib-1.3.1-h4ab18f5_1.conda#57d7dc60e9325e3de37ff8dffd18e814 https://conda.anaconda.org/conda-forge/linux-64/make-4.3-hd18ef5c_1.tar.bz2#4049ebfd3190b580dffe76daed26155a https://conda.anaconda.org/conda-forge/linux-64/ncurses-6.5-h59595ed_0.conda#fcea371545eda051b6deafb24889fc69 -https://conda.anaconda.org/conda-forge/linux-64/openssl-3.3.1-h4ab18f5_1.conda#b1e9d076f14e8d776213fd5047b4c3d9 +https://conda.anaconda.org/conda-forge/linux-64/openssl-3.3.1-h4bc722e_2.conda#e1b454497f9f7c1147fdde4b53f1b512 https://conda.anaconda.org/conda-forge/linux-64/pthread-stubs-0.4-h36c2ea0_1001.tar.bz2#22dad4df6e8630e8dff2428f6f6a7036 https://conda.anaconda.org/conda-forge/linux-64/sed-4.8-he412f7d_0.tar.bz2#7362f0042e95681f5d371c46c83ebd08 https://conda.anaconda.org/conda-forge/linux-64/xorg-kbproto-1.0.7-h7f98852_1002.tar.bz2#4b230e8381279d76131116660f5a241a @@ -55,7 +55,7 @@ https://conda.anaconda.org/conda-forge/linux-64/xorg-xproto-7.0.31-h7f98852_1007 https://conda.anaconda.org/conda-forge/linux-64/xz-5.2.6-h166bdaf_0.tar.bz2#2161070d867d1b1204ea749c8eec4ef0 https://conda.anaconda.org/conda-forge/linux-64/expat-2.6.2-h59595ed_0.conda#53fb86322bdb89496d7579fe3f02fd61 https://conda.anaconda.org/conda-forge/linux-64/graphite2-1.3.13-h59595ed_1003.conda#f87c7b7c2cb45f323ffbce941c78ab7c -https://conda.anaconda.org/conda-forge/linux-64/icu-73.2-h59595ed_0.conda#cc47e1facc155f91abd89b11e48e72ff +https://conda.anaconda.org/conda-forge/linux-64/icu-75.1-he02047a_0.conda#8b189310083baabfb622af68fd9d3ae3 https://conda.anaconda.org/conda-forge/linux-64/lerc-4.0.0-h27087fc_0.tar.bz2#76bbff344f0134279f225174e9064c8f https://conda.anaconda.org/conda-forge/linux-64/libedit-3.1.20191231-he28a2e2_2.tar.bz2#4d331e44109e3f0e19b4cb8f9b82f3e1 https://conda.anaconda.org/conda-forge/linux-64/libgfortran-ng-14.1.0-h69a702a_0.conda#f4ca84fbd6d06b0a052fb2d5b96dde41 @@ -65,7 +65,7 @@ https://conda.anaconda.org/conda-forge/linux-64/libsanitizer-14.1.0-hcba0ae0_0.c https://conda.anaconda.org/conda-forge/linux-64/libsqlite-3.46.0-hde9e2c9_0.conda#18aa975d2094c34aef978060ae7da7d8 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+https://conda.anaconda.org/conda-forge/linux-64/r-glue-1.7.0-r44hb1dbf0f_1.conda#353c728f5a70cb0c530c01c47cc6bb66 +https://conda.anaconda.org/conda-forge/noarch/r-gsalib-2.2.1-r44hc72bb7e_3.conda#4c13b89540896e44cee48069cf2ff704 +https://conda.anaconda.org/conda-forge/linux-64/r-gtools-3.9.5-r44hb1dbf0f_1.conda#40f5e42c4673ad0187907d821f44c7e5 +https://conda.anaconda.org/conda-forge/linux-64/r-isoband-0.2.7-r44ha18555a_3.conda#4745fadbe3c521e46d9c9b39148ac3c7 +https://conda.anaconda.org/conda-forge/linux-64/r-kernsmooth-2.23_24-r44hc2011d3_1.conda#fa86b7628e4b5f609bd40cce8a7ae801 +https://conda.anaconda.org/conda-forge/noarch/r-labeling-0.4.3-r44hc72bb7e_1.conda#49f2c043dfb8f5003dea36ae39ca1103 +https://conda.anaconda.org/conda-forge/linux-64/r-lattice-0.22_6-r44hb1dbf0f_1.conda#507b46f5005deff049c88453165b30d3 +https://conda.anaconda.org/conda-forge/linux-64/r-magrittr-2.0.3-r44hb1dbf0f_3.conda#a53562b6400cbbf0323fb97881ba61b3 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+https://conda.anaconda.org/conda-forge/noarch/r-withr-3.0.1-r44hc72bb7e_0.conda#b9171dfd69c9d0e35ffc8927f79e447f +https://conda.anaconda.org/conda-forge/linux-64/r-catools-1.18.2-r44ha18555a_3.conda#82ce8ed9e8dc9a2f818d89fcf27d4e8f +https://conda.anaconda.org/conda-forge/linux-64/r-ellipsis-0.3.2-r44hb1dbf0f_3.conda#a96cb6b4b61efd45ffe47019af5eb879 +https://conda.anaconda.org/conda-forge/noarch/r-lifecycle-1.0.4-r44hc72bb7e_1.conda#66d0ba7c05d0abfa11d126ba8e2907aa +https://conda.anaconda.org/conda-forge/linux-64/r-matrix-1.6_5-r44he966344_1.conda#bbcb8fe02b64b3b69bf078f2020f7446 +https://conda.anaconda.org/conda-forge/noarch/r-munsell-0.5.1-r44hc72bb7e_1.conda#871dfde2639a8fdfe210eea7c59fd1e8 +https://conda.anaconda.org/conda-forge/linux-64/r-nlme-3.1_165-r44hbcb9c34_1.conda#b579f3ffba329dd5b46bddb429a8aa2e +https://conda.anaconda.org/conda-forge/linux-64/r-plyr-1.8.9-r44ha18555a_1.conda#4d48c0a215274a331bde69cc65a932d2 +https://conda.anaconda.org/conda-forge/noarch/r-gplots-3.1.3.1-r44hc72bb7e_1.conda#d662367291002b1e449f36ef26980cb4 +https://conda.anaconda.org/conda-forge/noarch/r-gtable-0.3.5-r44hc72bb7e_1.conda#c3040db0b657a19a071ed472d24a204d +https://conda.anaconda.org/conda-forge/linux-64/r-mgcv-1.9_1-r44h0d28552_1.conda#3bd992bc484600de3b23809fb76eb7bb +https://conda.anaconda.org/conda-forge/linux-64/r-reshape-0.8.9-r44hc72bb7e_3.conda#76e52127f959b28ff3c41b0493f88b38 +https://conda.anaconda.org/conda-forge/noarch/r-scales-1.3.0-r44hc72bb7e_1.conda#31cda9180dde0613a04a020771eb2d09 +https://conda.anaconda.org/conda-forge/linux-64/r-vctrs-0.6.5-r44h0d4f4ea_1.conda#399bc7872bdb40b5531d887858253e76 +https://conda.anaconda.org/conda-forge/noarch/r-pillar-1.9.0-r44hc72bb7e_2.conda#3ec6418c9af0a90d4513cadfe0ef863a +https://conda.anaconda.org/conda-forge/linux-64/r-tibble-3.2.1-r44hdb488b9_3.conda#03203ac70558ba5bb836d1cb641f1b87 +https://conda.anaconda.org/conda-forge/noarch/r-ggplot2-3.5.1-r44hc72bb7e_1.conda#c6209f7de229696ebd0086e7c27a02ac https://conda.anaconda.org/bioconda/noarch/gatk-3.8-hdfd78af_12.tar.bz2#ce94fe85517155af78e62d1412785d7e diff --git a/bio/gatk3/baserecalibrator/environment.yaml b/bio/gatk3/baserecalibrator/environment.yaml index eaa654dc24a..cfa44daec8d 100644 --- a/bio/gatk3/baserecalibrator/environment.yaml +++ b/bio/gatk3/baserecalibrator/environment.yaml @@ -4,5 +4,5 @@ channels: - nodefaults dependencies: - gatk =3.8 - - python =3.12.4 + - python =3.12.5 - snakemake-wrapper-utils =0.6.2 From fe33c2c27328212c528e94f995fd0bc26d7fde39 Mon Sep 17 00:00:00 2001 From: "snakedeploy-bot[bot]" <115615832+snakedeploy-bot[bot]@users.noreply.github.com> Date: Fri, 16 Aug 2024 03:29:40 +0000 Subject: [PATCH 48/62] perf: autobump bio/igv-reports (#3120) Automatic bump of bio/igv-reports. ## Summary by CodeRabbit - **New Features** - Upgraded the `igv-reports` dependency to version 1.13.0, potentially introducing enhancements and new functionalities. - **Maintenance Updates** - Updated multiple package dependencies to their latest versions for improved security, stability, and performance. - Removed deprecated packages and streamlined dependencies for better management and compatibility. - Adjusted package URLs to ensure accurate fetching during environment setup. --------- Co-authored-by: snakedeploy-bot[bot] <115615832+snakedeploy-bot[bot]@users.noreply.github.com> --- bio/igv-reports/environment.linux-64.pin.txt | 62 +++++++++++--------- bio/igv-reports/environment.yaml | 2 +- 2 files changed, 35 insertions(+), 29 deletions(-) diff --git a/bio/igv-reports/environment.linux-64.pin.txt b/bio/igv-reports/environment.linux-64.pin.txt index 05a95099a92..c6f1de727aa 100644 --- a/bio/igv-reports/environment.linux-64.pin.txt +++ b/bio/igv-reports/environment.linux-64.pin.txt @@ -3,49 +3,55 @@ # platform: linux-64 @EXPLICIT https://conda.anaconda.org/conda-forge/linux-64/_libgcc_mutex-0.1-conda_forge.tar.bz2#d7c89558ba9fa0495403155b64376d81 -https://conda.anaconda.org/conda-forge/linux-64/ca-certificates-2024.2.2-hbcca054_0.conda#2f4327a1cbe7f022401b236e915a5fef -https://conda.anaconda.org/conda-forge/linux-64/ld_impl_linux-64-2.40-h41732ed_0.conda#7aca3059a1729aa76c597603f10b0dd3 -https://conda.anaconda.org/conda-forge/linux-64/libstdcxx-ng-13.2.0-h7e041cc_5.conda#f6f6600d18a4047b54f803cf708b868a -https://conda.anaconda.org/conda-forge/linux-64/python_abi-3.10-4_cp310.conda#26322ec5d7712c3ded99dd656142b8ce +https://conda.anaconda.org/conda-forge/linux-64/ca-certificates-2024.7.4-hbcca054_0.conda#23ab7665c5f63cfb9f1f6195256daac6 +https://conda.anaconda.org/conda-forge/linux-64/ld_impl_linux-64-2.40-hf3520f5_7.conda#b80f2f396ca2c28b8c14c437a4ed1e74 +https://conda.anaconda.org/conda-forge/linux-64/python_abi-3.12-4_cp312.conda#dccc2d142812964fcc6abdc97b672dff https://conda.anaconda.org/conda-forge/noarch/tzdata-2024a-h0c530f3_0.conda#161081fc7cec0bfda0d86d7cb595f8d8 -https://conda.anaconda.org/conda-forge/linux-64/libgomp-13.2.0-h807b86a_5.conda#d211c42b9ce49aee3734fdc828731689 +https://conda.anaconda.org/conda-forge/linux-64/libgomp-14.1.0-h77fa898_0.conda#ae061a5ed5f05818acdf9adab72c146d https://conda.anaconda.org/conda-forge/linux-64/_openmp_mutex-4.5-2_gnu.tar.bz2#73aaf86a425cc6e73fcf236a5a46396d -https://conda.anaconda.org/conda-forge/linux-64/libgcc-ng-13.2.0-h807b86a_5.conda#d4ff227c46917d3b4565302a2bbb276b -https://conda.anaconda.org/conda-forge/linux-64/bzip2-1.0.8-hd590300_5.conda#69b8b6202a07720f448be700e300ccf4 -https://conda.anaconda.org/conda-forge/linux-64/c-ares-1.26.0-hd590300_0.conda#a86d90025198fd411845fc245ebc06c8 +https://conda.anaconda.org/conda-forge/linux-64/libgcc-ng-14.1.0-h77fa898_0.conda#ca0fad6a41ddaef54a153b78eccb5037 +https://conda.anaconda.org/conda-forge/linux-64/bzip2-1.0.8-h4bc722e_7.conda#62ee74e96c5ebb0af99386de58cf9553 +https://conda.anaconda.org/conda-forge/linux-64/c-ares-1.33.0-ha66036c_0.conda#b6927f788e85267beef6cbb292aaebdd https://conda.anaconda.org/conda-forge/linux-64/keyutils-1.6.1-h166bdaf_0.tar.bz2#30186d27e2c9fa62b45fb1476b7200e3 -https://conda.anaconda.org/conda-forge/linux-64/libdeflate-1.18-h0b41bf4_0.conda#6aa9c9de5542ecb07fdda9ca626252d8 +https://conda.anaconda.org/conda-forge/linux-64/libdeflate-1.21-h4bc722e_0.conda#36ce76665bf67f5aac36be7a0d21b7f3 https://conda.anaconda.org/conda-forge/linux-64/libev-4.33-hd590300_2.conda#172bf1cd1ff8629f2b1179945ed45055 +https://conda.anaconda.org/conda-forge/linux-64/libexpat-2.6.2-h59595ed_0.conda#e7ba12deb7020dd080c6c70e7b6f6a3d https://conda.anaconda.org/conda-forge/linux-64/libffi-3.4.2-h7f98852_5.tar.bz2#d645c6d2ac96843a2bfaccd2d62b3ac3 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+https://conda.anaconda.org/bioconda/noarch/igv-reports-1.13.0-pyh7e72e81_0.tar.bz2#014155080b999b9d2972a0863d396dc3 diff --git a/bio/igv-reports/environment.yaml b/bio/igv-reports/environment.yaml index fa167fa43b5..4e8972bc334 100644 --- a/bio/igv-reports/environment.yaml +++ b/bio/igv-reports/environment.yaml @@ -3,4 +3,4 @@ channels: - bioconda - nodefaults dependencies: - - igv-reports =1.12.0 + - igv-reports =1.13.0 From 62b0231c99920200e3fa6794f87578869cc35bd5 Mon Sep 17 00:00:00 2001 From: "snakedeploy-bot[bot]" <115615832+snakedeploy-bot[bot]@users.noreply.github.com> Date: Fri, 16 Aug 2024 05:29:52 +0000 Subject: [PATCH 49/62] perf: autobump bio/trinity (#3121) Automatic bump of bio/trinity. ## Summary by CodeRabbit - **New Features** - Updated dependencies for improved performance and compatibility, including key packages like `ca-certificates`, `libgcc`, and `libstdcxx`. - Introduced new version of `pandoc` for enhanced document processing capabilities. - **Bug Fixes** - Minor update to the `trinity` package to potentially resolve issues and improve functionality. --------- Co-authored-by: snakedeploy-bot[bot] <115615832+snakedeploy-bot[bot]@users.noreply.github.com> --- bio/trinity/environment.linux-64.pin.txt | 611 ++++++++++++----------- bio/trinity/environment.yaml | 2 +- 2 files changed, 332 insertions(+), 281 deletions(-) diff --git a/bio/trinity/environment.linux-64.pin.txt b/bio/trinity/environment.linux-64.pin.txt index 5ce5dabbcba..b4ff1de3056 100644 --- a/bio/trinity/environment.linux-64.pin.txt +++ b/bio/trinity/environment.linux-64.pin.txt @@ -4,59 +4,53 @@ @EXPLICIT https://conda.anaconda.org/conda-forge/linux-64/_libgcc_mutex-0.1-conda_forge.tar.bz2#d7c89558ba9fa0495403155b64376d81 https://conda.anaconda.org/conda-forge/noarch/_r-mutex-1.0.1-anacondar_1.tar.bz2#19f9db5f4f1b7f5ef5f6d67207f25f38 -https://conda.anaconda.org/conda-forge/linux-64/ca-certificates-2023.7.22-hbcca054_0.conda#a73ecd2988327ad4c8f2c331482917f2 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From: Felix Wiegand Date: Wed, 21 Aug 2024 10:39:10 +0200 Subject: [PATCH 50/62] feat: Allow outputting of rendered yte config in Datavzrd wrapper (#3123) MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit ### QC * [ ] I confirm that I have followed the [documentation for contributing to `snakemake-wrappers`](https://snakemake-wrappers.readthedocs.io/en/stable/contributing.html). While the contributions guidelines are more extensive, please particularly ensure that: * [ ] `test.py` was updated to call any added or updated example rules in a `Snakefile` * [ ] `input:` and `output:` file paths in the rules can be chosen arbitrarily * [ ] wherever possible, command line arguments are inferred and set automatically (e.g. based on file extensions in `input:` or `output:`) * [ ] temporary files are either written to a unique hidden folder in the working directory, or (better) stored where the Python function `tempfile.gettempdir()` points to * [ ] the `meta.yaml` contains a link to the documentation of the respective tool or command under `url:` * [ ] conda environments use a minimal amount of channels and packages, in recommended ordering ## Summary by CodeRabbit - **New Features** - Added an optional output configuration file in YAML format for enhanced tracking of pipeline parameters and settings. - Implemented functionality to save processed data to a specified output configuration path, improving workflow management. - Enhanced metadata in the configuration file with additional context regarding the output structure and location. --------- Co-authored-by: Johannes Köster --- utils/datavzrd/meta.yaml | 2 ++ utils/datavzrd/test/Snakefile | 2 ++ utils/datavzrd/wrapper.py | 3 +++ 3 files changed, 7 insertions(+) diff --git a/utils/datavzrd/meta.yaml b/utils/datavzrd/meta.yaml index 29f7caa14a1..a9a3c6f9907 100644 --- a/utils/datavzrd/meta.yaml +++ b/utils/datavzrd/meta.yaml @@ -6,5 +6,7 @@ description: | Any files specified in the configuration file have to be also specified as additional input files in the datavzrd rule. url: https://github.com/datavzrd/datavzrd +output: +- config: Path to the rendered yte config authors: - Felix Mölder diff --git a/utils/datavzrd/test/Snakefile b/utils/datavzrd/test/Snakefile index 03b70eba313..6c9eaef0158 100644 --- a/utils/datavzrd/test/Snakefile +++ b/utils/datavzrd/test/Snakefile @@ -21,6 +21,8 @@ rule datavzrd: # see https://snakemake.readthedocs.io/en/stable/snakefiles/reporting.html # for additional options like caption, categories and labels ), + # optionally output the rendered config + config = "resources/datavzrd/{sample}.rendered_config.yaml" log: "logs/datavzrd_report/{sample}.log", wrapper: diff --git a/utils/datavzrd/wrapper.py b/utils/datavzrd/wrapper.py index d0138a287f8..03dd330d974 100644 --- a/utils/datavzrd/wrapper.py +++ b/utils/datavzrd/wrapper.py @@ -6,6 +6,7 @@ import tempfile from yte import process_yaml from snakemake.shell import shell +import shutil log = snakemake.log_fmt_shell(stdout=True, stderr=True) @@ -27,4 +28,6 @@ ) processed.flush() + if snakemake.output.config: + shutil.copy(processed.name, snakemake.output.config) shell("datavzrd {processed.name} {extra} --output {snakemake.output[0]} {log}") From 51014613939bfc5e48e0b2ae619e283cf36bfd88 Mon Sep 17 00:00:00 2001 From: Felix Wiegand Date: Wed, 21 Aug 2024 10:52:22 +0200 Subject: [PATCH 51/62] perf: Update Datavzrd wrapper (#3122) ### QC * [ ] I confirm that I have followed the [documentation for contributing to `snakemake-wrappers`](https://snakemake-wrappers.readthedocs.io/en/stable/contributing.html). While the contributions guidelines are more extensive, please particularly ensure that: * [ ] `test.py` was updated to call any added or updated example rules in a `Snakefile` * [ ] `input:` and `output:` file paths in the rules can be chosen arbitrarily * [ ] wherever possible, command line arguments are inferred and set automatically (e.g. based on file extensions in `input:` or `output:`) * [ ] temporary files are either written to a unique hidden folder in the working directory, or (better) stored where the Python function `tempfile.gettempdir()` points to * [ ] the `meta.yaml` contains a link to the documentation of the respective tool or command under `url:` * [ ] conda environments use a minimal amount of channels and packages, in recommended ordering ## Summary by CodeRabbit - **New Features** - Updated the `datavzrd` package to the latest version, potentially enhancing performance and adding new functionalities. - **Bug Fixes** - Upgrading to the new version may resolve existing issues from the prior version. --- utils/datavzrd/environment.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/utils/datavzrd/environment.yaml b/utils/datavzrd/environment.yaml index 0409c9f2a0a..a0f842dcd7e 100644 --- a/utils/datavzrd/environment.yaml +++ b/utils/datavzrd/environment.yaml @@ -2,5 +2,5 @@ channels: - conda-forge - nodefaults dependencies: - - datavzrd =2.41.1 + - datavzrd =2.41.2 - yte =1.5.4 From 51860ab7f5a91a071cbcbc396d472bcbcf8a982e Mon Sep 17 00:00:00 2001 From: "github-actions[bot]" <41898282+github-actions[bot]@users.noreply.github.com> Date: Wed, 21 Aug 2024 11:19:47 +0200 Subject: [PATCH 52/62] chore: release 4.1.0 (#3124) :robot: I have created a release \*beep\* \*boop\* --- ## [4.1.0](https://www.github.com/snakemake/snakemake-wrappers/compare/v4.0.0...v4.1.0) (2024-08-21) ### Features * Allow outputting of rendered yte config in Datavzrd wrapper ([#3123](https://www.github.com/snakemake/snakemake-wrappers/issues/3123)) ([e74be78](https://www.github.com/snakemake/snakemake-wrappers/commit/e74be7843299478a276febfacb52825a9762500c)) ### Bug Fixes * Correctly handle non str index list for bwa-mem2/mem ([#3101](https://www.github.com/snakemake/snakemake-wrappers/issues/3101)) ([6f46508](https://www.github.com/snakemake/snakemake-wrappers/commit/6f46508aa99663930e70c82114205929aee2dfcb)) ### Performance Improvements * autobump bio/gatk3/baserecalibrator ([#3119](https://www.github.com/snakemake/snakemake-wrappers/issues/3119)) ([6c2bdfd](https://www.github.com/snakemake/snakemake-wrappers/commit/6c2bdfdca79c7037448bc601a4aeb3d578ea0980)) * autobump bio/gatk3/realignertargetcreator ([#3118](https://www.github.com/snakemake/snakemake-wrappers/issues/3118)) ([ba219e7](https://www.github.com/snakemake/snakemake-wrappers/commit/ba219e7698eb078fe22c703a9662c8cb6deee0eb)) * autobump bio/genomescope ([#3117](https://www.github.com/snakemake/snakemake-wrappers/issues/3117)) ([6292229](https://www.github.com/snakemake/snakemake-wrappers/commit/62922298404397c7b23dc5b8fb01bc33e445e97f)) * autobump bio/igv-reports ([#3120](https://www.github.com/snakemake/snakemake-wrappers/issues/3120)) ([fe33c2c](https://www.github.com/snakemake/snakemake-wrappers/commit/fe33c2c27328212c528e94f995fd0bc26d7fde39)) * autobump bio/trinity ([#3121](https://www.github.com/snakemake/snakemake-wrappers/issues/3121)) ([62b0231](https://www.github.com/snakemake/snakemake-wrappers/commit/62b0231c99920200e3fa6794f87578869cc35bd5)) * Update Datavzrd wrapper ([#3122](https://www.github.com/snakemake/snakemake-wrappers/issues/3122)) ([5101461](https://www.github.com/snakemake/snakemake-wrappers/commit/51014613939bfc5e48e0b2ae619e283cf36bfd88)) --- This PR was generated with [Release Please](https://github.com/googleapis/release-please). See [documentation](https://github.com/googleapis/release-please#release-please). Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> --- CHANGELOG.md | 22 ++++++++++++++++++++++ 1 file changed, 22 insertions(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 0279434bd9e..9cab567dea2 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -1,5 +1,27 @@ # Changelog +## [4.1.0](https://www.github.com/snakemake/snakemake-wrappers/compare/v4.0.0...v4.1.0) (2024-08-21) + + +### Features + +* Allow outputting of rendered yte config in Datavzrd wrapper ([#3123](https://www.github.com/snakemake/snakemake-wrappers/issues/3123)) ([e74be78](https://www.github.com/snakemake/snakemake-wrappers/commit/e74be7843299478a276febfacb52825a9762500c)) + + +### Bug Fixes + +* Correctly handle non str index list for bwa-mem2/mem ([#3101](https://www.github.com/snakemake/snakemake-wrappers/issues/3101)) ([6f46508](https://www.github.com/snakemake/snakemake-wrappers/commit/6f46508aa99663930e70c82114205929aee2dfcb)) + + +### Performance Improvements + +* autobump bio/gatk3/baserecalibrator ([#3119](https://www.github.com/snakemake/snakemake-wrappers/issues/3119)) ([6c2bdfd](https://www.github.com/snakemake/snakemake-wrappers/commit/6c2bdfdca79c7037448bc601a4aeb3d578ea0980)) +* autobump bio/gatk3/realignertargetcreator ([#3118](https://www.github.com/snakemake/snakemake-wrappers/issues/3118)) ([ba219e7](https://www.github.com/snakemake/snakemake-wrappers/commit/ba219e7698eb078fe22c703a9662c8cb6deee0eb)) +* autobump bio/genomescope ([#3117](https://www.github.com/snakemake/snakemake-wrappers/issues/3117)) ([6292229](https://www.github.com/snakemake/snakemake-wrappers/commit/62922298404397c7b23dc5b8fb01bc33e445e97f)) +* autobump bio/igv-reports ([#3120](https://www.github.com/snakemake/snakemake-wrappers/issues/3120)) ([fe33c2c](https://www.github.com/snakemake/snakemake-wrappers/commit/fe33c2c27328212c528e94f995fd0bc26d7fde39)) +* autobump bio/trinity ([#3121](https://www.github.com/snakemake/snakemake-wrappers/issues/3121)) ([62b0231](https://www.github.com/snakemake/snakemake-wrappers/commit/62b0231c99920200e3fa6794f87578869cc35bd5)) +* Update Datavzrd wrapper ([#3122](https://www.github.com/snakemake/snakemake-wrappers/issues/3122)) ([5101461](https://www.github.com/snakemake/snakemake-wrappers/commit/51014613939bfc5e48e0b2ae619e283cf36bfd88)) + ## [4.0.0](https://www.github.com/snakemake/snakemake-wrappers/compare/v3.14.2...v4.0.0) (2024-08-14) From 5bd032cfa2a24eaa66cb7e24f5b3439fae939886 Mon Sep 17 00:00:00 2001 From: Felix Wiegand Date: Wed, 21 Aug 2024 12:09:56 +0200 Subject: [PATCH 53/62] fix: Fix datavzrd wrapper (#3125) MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit ### QC * [ ] I confirm that I have followed the [documentation for contributing to `snakemake-wrappers`](https://snakemake-wrappers.readthedocs.io/en/stable/contributing.html). While the contributions guidelines are more extensive, please particularly ensure that: * [ ] `test.py` was updated to call any added or updated example rules in a `Snakefile` * [ ] `input:` and `output:` file paths in the rules can be chosen arbitrarily * [ ] wherever possible, command line arguments are inferred and set automatically (e.g. based on file extensions in `input:` or `output:`) * [ ] temporary files are either written to a unique hidden folder in the working directory, or (better) stored where the Python function `tempfile.gettempdir()` points to * [ ] the `meta.yaml` contains a link to the documentation of the respective tool or command under `url:` * [ ] conda environments use a minimal amount of channels and packages, in recommended ordering ## Summary by CodeRabbit - **Bug Fixes** - Improved logic for determining the existence of configuration output, enhancing the app's flexibility in handling outputs. --------- Co-authored-by: Johannes Köster --- utils/datavzrd/wrapper.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/utils/datavzrd/wrapper.py b/utils/datavzrd/wrapper.py index 03dd330d974..aeaee55b306 100644 --- a/utils/datavzrd/wrapper.py +++ b/utils/datavzrd/wrapper.py @@ -28,6 +28,6 @@ ) processed.flush() - if snakemake.output.config: - shutil.copy(processed.name, snakemake.output.config) + if config_out := snakemake.output.get("config"): + shutil.copy(processed.name, config_out) shell("datavzrd {processed.name} {extra} --output {snakemake.output[0]} {log}") From 92dbf03c066b04956aee5bbee19c137831b47f7e Mon Sep 17 00:00:00 2001 From: "github-actions[bot]" <41898282+github-actions[bot]@users.noreply.github.com> Date: Wed, 21 Aug 2024 12:37:44 +0200 Subject: [PATCH 54/62] chore: release 4.1.1 (#3126) :robot: I have created a release \*beep\* \*boop\* --- ### [4.1.1](https://www.github.com/snakemake/snakemake-wrappers/compare/v4.1.0...v4.1.1) (2024-08-21) ### Bug Fixes * Fix datavzrd wrapper ([#3125](https://www.github.com/snakemake/snakemake-wrappers/issues/3125)) ([5bd032c](https://www.github.com/snakemake/snakemake-wrappers/commit/5bd032cfa2a24eaa66cb7e24f5b3439fae939886)) --- This PR was generated with [Release Please](https://github.com/googleapis/release-please). See [documentation](https://github.com/googleapis/release-please#release-please). Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> --- CHANGELOG.md | 7 +++++++ 1 file changed, 7 insertions(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 9cab567dea2..fff71d9e785 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -1,5 +1,12 @@ # Changelog +### [4.1.1](https://www.github.com/snakemake/snakemake-wrappers/compare/v4.1.0...v4.1.1) (2024-08-21) + + +### Bug Fixes + +* Fix datavzrd wrapper ([#3125](https://www.github.com/snakemake/snakemake-wrappers/issues/3125)) ([5bd032c](https://www.github.com/snakemake/snakemake-wrappers/commit/5bd032cfa2a24eaa66cb7e24f5b3439fae939886)) + ## [4.1.0](https://www.github.com/snakemake/snakemake-wrappers/compare/v4.0.0...v4.1.0) (2024-08-21) From a9bd6dfdeee5692c76507148e12e81547c0c0906 Mon Sep 17 00:00:00 2001 From: "snakedeploy-bot[bot]" <115615832+snakedeploy-bot[bot]@users.noreply.github.com> Date: Fri, 23 Aug 2024 01:40:55 +0000 Subject: [PATCH 55/62] perf: autobump bio/bbtools (#3127) Automatic bump of bio/bbtools. ## Summary by CodeRabbit - **New Features** - Updated package dependencies to include newer versions, enhancing compatibility and performance. - Introduced updated versions of key libraries such as `openssl`, `zlib`, and `cairo`. - **Bug Fixes** - Upgraded `bbmap` from version `39.06` to `39.08`, potentially improving functionality for bioinformatics tasks. - **Chores** - Cleaned up and consolidated dependencies by removing outdated packages and updating build numbers. --------- Co-authored-by: snakedeploy-bot[bot] <115615832+snakedeploy-bot[bot]@users.noreply.github.com> --- bio/bbtools/environment.linux-64.pin.txt | 96 ++++++++++++------------ bio/bbtools/environment.yaml | 2 +- 2 files changed, 48 insertions(+), 50 deletions(-) diff --git a/bio/bbtools/environment.linux-64.pin.txt b/bio/bbtools/environment.linux-64.pin.txt index 882a2f8a0aa..6ec6d449fa7 100644 --- a/bio/bbtools/environment.linux-64.pin.txt +++ b/bio/bbtools/environment.linux-64.pin.txt @@ -3,42 +3,37 @@ # platform: linux-64 @EXPLICIT https://conda.anaconda.org/conda-forge/linux-64/_libgcc_mutex-0.1-conda_forge.tar.bz2#d7c89558ba9fa0495403155b64376d81 -https://conda.anaconda.org/conda-forge/linux-64/ca-certificates-2023.11.17-hbcca054_0.conda#01ffc8d36f9eba0ce0b3c1955fa780ee +https://conda.anaconda.org/conda-forge/linux-64/ca-certificates-2024.7.4-hbcca054_0.conda#23ab7665c5f63cfb9f1f6195256daac6 https://conda.anaconda.org/conda-forge/noarch/font-ttf-dejavu-sans-mono-2.37-hab24e00_0.tar.bz2#0c96522c6bdaed4b1566d11387caaf45 https://conda.anaconda.org/conda-forge/noarch/font-ttf-inconsolata-3.000-h77eed37_0.tar.bz2#34893075a5c9e55cdafac56607368fc6 https://conda.anaconda.org/conda-forge/noarch/font-ttf-source-code-pro-2.038-h77eed37_0.tar.bz2#4d59c254e01d9cde7957100457e2d5fb -https://conda.anaconda.org/conda-forge/noarch/font-ttf-ubuntu-0.83-h77eed37_1.conda#6185f640c43843e5ad6fd1c5372c3f80 -https://conda.anaconda.org/conda-forge/linux-64/ld_impl_linux-64-2.40-h41732ed_0.conda#7aca3059a1729aa76c597603f10b0dd3 -https://conda.anaconda.org/conda-forge/linux-64/libstdcxx-ng-13.2.0-h7e041cc_5.conda#f6f6600d18a4047b54f803cf708b868a -https://conda.anaconda.org/conda-forge/noarch/tzdata-2023d-h0c530f3_0.conda#8dee24b8be2d9ff81e7bd4d7d97ff1b0 +https://conda.anaconda.org/conda-forge/noarch/font-ttf-ubuntu-0.83-h77eed37_2.conda#cbbe59391138ea5ad3658c76912e147f +https://conda.anaconda.org/conda-forge/linux-64/ld_impl_linux-64-2.40-hf3520f5_7.conda#b80f2f396ca2c28b8c14c437a4ed1e74 +https://conda.anaconda.org/conda-forge/noarch/tzdata-2024a-h0c530f3_0.conda#161081fc7cec0bfda0d86d7cb595f8d8 https://conda.anaconda.org/conda-forge/noarch/fonts-conda-forge-1-0.tar.bz2#f766549260d6815b0c52253f1fb1bb29 -https://conda.anaconda.org/conda-forge/linux-64/libgomp-13.2.0-h807b86a_5.conda#d211c42b9ce49aee3734fdc828731689 +https://conda.anaconda.org/conda-forge/linux-64/libgomp-14.1.0-h77fa898_0.conda#ae061a5ed5f05818acdf9adab72c146d https://conda.anaconda.org/conda-forge/linux-64/_openmp_mutex-4.5-2_gnu.tar.bz2#73aaf86a425cc6e73fcf236a5a46396d https://conda.anaconda.org/conda-forge/noarch/fonts-conda-ecosystem-1-0.tar.bz2#fee5683a3f04bd15cbd8318b096a27ab -https://conda.anaconda.org/conda-forge/linux-64/libgcc-ng-13.2.0-h807b86a_5.conda#d4ff227c46917d3b4565302a2bbb276b -https://conda.anaconda.org/conda-forge/linux-64/alsa-lib-1.2.10-hd590300_0.conda#75dae9a4201732aa78a530b826ee5fe0 -https://conda.anaconda.org/conda-forge/linux-64/bzip2-1.0.8-hd590300_5.conda#69b8b6202a07720f448be700e300ccf4 -https://conda.anaconda.org/conda-forge/linux-64/c-ares-1.26.0-hd590300_0.conda#a86d90025198fd411845fc245ebc06c8 -https://conda.anaconda.org/conda-forge/linux-64/gettext-0.21.1-h27087fc_0.tar.bz2#14947d8770185e5153fdd04d4673ed37 -https://conda.anaconda.org/conda-forge/linux-64/giflib-5.2.1-h0b41bf4_3.conda#96f3b11872ef6fad973eac856cd2624f -https://conda.anaconda.org/conda-forge/linux-64/graphite2-1.3.13-h58526e2_1001.tar.bz2#8c54672728e8ec6aa6db90cf2806d220 -https://conda.anaconda.org/conda-forge/linux-64/icu-73.2-h59595ed_0.conda#cc47e1facc155f91abd89b11e48e72ff +https://conda.anaconda.org/conda-forge/linux-64/libgcc-ng-14.1.0-h77fa898_0.conda#ca0fad6a41ddaef54a153b78eccb5037 +https://conda.anaconda.org/conda-forge/linux-64/alsa-lib-1.2.12-h4ab18f5_0.conda#7ed427f0871fd41cb1d9c17727c17589 +https://conda.anaconda.org/conda-forge/linux-64/bzip2-1.0.8-h4bc722e_7.conda#62ee74e96c5ebb0af99386de58cf9553 +https://conda.anaconda.org/conda-forge/linux-64/c-ares-1.33.0-ha66036c_0.conda#b6927f788e85267beef6cbb292aaebdd +https://conda.anaconda.org/conda-forge/linux-64/giflib-5.2.2-hd590300_0.conda#3bf7b9fd5a7136126e0234db4b87c8b6 https://conda.anaconda.org/conda-forge/linux-64/keyutils-1.6.1-h166bdaf_0.tar.bz2#30186d27e2c9fa62b45fb1476b7200e3 -https://conda.anaconda.org/conda-forge/linux-64/lerc-4.0.0-h27087fc_0.tar.bz2#76bbff344f0134279f225174e9064c8f -https://conda.anaconda.org/conda-forge/linux-64/libdeflate-1.18-h0b41bf4_0.conda#6aa9c9de5542ecb07fdda9ca626252d8 +https://conda.anaconda.org/conda-forge/linux-64/libdeflate-1.21-h4bc722e_0.conda#36ce76665bf67f5aac36be7a0d21b7f3 https://conda.anaconda.org/conda-forge/linux-64/libev-4.33-hd590300_2.conda#172bf1cd1ff8629f2b1179945ed45055 -https://conda.anaconda.org/conda-forge/linux-64/libexpat-2.5.0-hcb278e6_1.conda#6305a3dd2752c76335295da4e581f2fd +https://conda.anaconda.org/conda-forge/linux-64/libexpat-2.6.2-h59595ed_0.conda#e7ba12deb7020dd080c6c70e7b6f6a3d https://conda.anaconda.org/conda-forge/linux-64/libffi-3.4.2-h7f98852_5.tar.bz2#d645c6d2ac96843a2bfaccd2d62b3ac3 https://conda.anaconda.org/conda-forge/linux-64/libiconv-1.17-hd590300_2.conda#d66573916ffcf376178462f1b61c941e -https://conda.anaconda.org/conda-forge/linux-64/libjpeg-turbo-2.1.5.1-hd590300_1.conda#323e90742f0f48fc22bea908735f55e6 +https://conda.anaconda.org/conda-forge/linux-64/libjpeg-turbo-3.0.0-hd590300_1.conda#ea25936bb4080d843790b586850f82b8 https://conda.anaconda.org/conda-forge/linux-64/libnsl-2.0.1-hd590300_0.conda#30fd6e37fe21f86f4bd26d6ee73eeec7 +https://conda.anaconda.org/conda-forge/linux-64/libstdcxx-ng-14.1.0-hc0a3c3a_0.conda#1cb187a157136398ddbaae90713e2498 https://conda.anaconda.org/conda-forge/linux-64/libuuid-2.38.1-h0b41bf4_0.conda#40b61aab5c7ba9ff276c41cfffe6b80b -https://conda.anaconda.org/conda-forge/linux-64/libwebp-base-1.3.2-hd590300_0.conda#30de3fd9b3b602f7473f30e684eeea8c +https://conda.anaconda.org/conda-forge/linux-64/libwebp-base-1.4.0-hd590300_0.conda#b26e8aa824079e1be0294e7152ca4559 https://conda.anaconda.org/conda-forge/linux-64/libxcrypt-4.4.36-hd590300_1.conda#5aa797f8787fe7a17d1b0821485b5adc -https://conda.anaconda.org/conda-forge/linux-64/libzlib-1.2.13-hd590300_5.conda#f36c115f1ee199da648e0597ec2047ad -https://conda.anaconda.org/conda-forge/linux-64/ncurses-6.4-h59595ed_2.conda#7dbaa197d7ba6032caf7ae7f32c1efa0 -https://conda.anaconda.org/conda-forge/linux-64/openssl-3.2.1-hd590300_0.conda#51a753e64a3027bd7e23a189b1f6e91e -https://conda.anaconda.org/conda-forge/linux-64/pixman-0.43.2-h59595ed_0.conda#71004cbf7924e19c02746ccde9fd7123 +https://conda.anaconda.org/conda-forge/linux-64/libzlib-1.3.1-h4ab18f5_1.conda#57d7dc60e9325e3de37ff8dffd18e814 +https://conda.anaconda.org/conda-forge/linux-64/ncurses-6.5-h59595ed_0.conda#fcea371545eda051b6deafb24889fc69 +https://conda.anaconda.org/conda-forge/linux-64/openssl-3.3.1-h4bc722e_2.conda#e1b454497f9f7c1147fdde4b53f1b512 https://conda.anaconda.org/conda-forge/linux-64/pthread-stubs-0.4-h36c2ea0_1001.tar.bz2#22dad4df6e8630e8dff2428f6f6a7036 https://conda.anaconda.org/conda-forge/linux-64/xorg-inputproto-2.3.2-h7f98852_1002.tar.bz2#bcd1b3396ec6960cbc1d2855a9e60b2b https://conda.anaconda.org/conda-forge/linux-64/xorg-kbproto-1.0.7-h7f98852_1002.tar.bz2#4b230e8381279d76131116660f5a241a @@ -50,45 +45,48 @@ https://conda.anaconda.org/conda-forge/linux-64/xorg-renderproto-0.11.1-h7f98852 https://conda.anaconda.org/conda-forge/linux-64/xorg-xextproto-7.3.0-h0b41bf4_1003.conda#bce9f945da8ad2ae9b1d7165a64d0f87 https://conda.anaconda.org/conda-forge/linux-64/xorg-xproto-7.0.31-h7f98852_1007.tar.bz2#b4a4381d54784606820704f7b5f05a15 https://conda.anaconda.org/conda-forge/linux-64/xz-5.2.6-h166bdaf_0.tar.bz2#2161070d867d1b1204ea749c8eec4ef0 -https://conda.anaconda.org/conda-forge/linux-64/expat-2.5.0-hcb278e6_1.conda#8b9b5aca60558d02ddaa09d599e55920 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pigz =2.8 From 97b2c9d218b120cda5991303f7b1b3d5b854bf2f Mon Sep 17 00:00:00 2001 From: "snakedeploy-bot[bot]" <115615832+snakedeploy-bot[bot]@users.noreply.github.com> Date: Fri, 23 Aug 2024 02:56:35 +0000 Subject: [PATCH 56/62] perf: autobump bio/gatk3/printreads (#3129) Automatic bump of bio/gatk3/printreads. ## Summary by CodeRabbit - **New Features** - Updated several packages in the environment to their latest versions, enhancing stability and compatibility. - Incremented Python version to 3.12.5 for improved functionality and bug fixes. - **Bug Fixes** - Various package updates may include critical fixes that enhance performance and security. - **Chores** - Removed outdated packages and introduced new dependencies to streamline the environment. --------- Co-authored-by: snakedeploy-bot[bot] <115615832+snakedeploy-bot[bot]@users.noreply.github.com> --- .../printreads/environment.linux-64.pin.txt | 133 +++++++++--------- bio/gatk3/printreads/environment.yaml | 2 +- 2 files changed, 68 insertions(+), 67 deletions(-) diff --git a/bio/gatk3/printreads/environment.linux-64.pin.txt b/bio/gatk3/printreads/environment.linux-64.pin.txt index 12c81bf584f..626ce6f8cf5 100644 --- a/bio/gatk3/printreads/environment.linux-64.pin.txt +++ b/bio/gatk3/printreads/environment.linux-64.pin.txt @@ -4,29 +4,30 @@ @EXPLICIT https://conda.anaconda.org/conda-forge/linux-64/_libgcc_mutex-0.1-conda_forge.tar.bz2#d7c89558ba9fa0495403155b64376d81 https://conda.anaconda.org/conda-forge/noarch/_r-mutex-1.0.1-anacondar_1.tar.bz2#19f9db5f4f1b7f5ef5f6d67207f25f38 +https://conda.anaconda.org/conda-forge/noarch/_sysroot_linux-64_curr_repodata_hack-3-h69a702a_16.conda#1c005af0c6ff22814b7c52ee448d4bea https://conda.anaconda.org/conda-forge/linux-64/ca-certificates-2024.7.4-hbcca054_0.conda#23ab7665c5f63cfb9f1f6195256daac6 https://conda.anaconda.org/conda-forge/noarch/font-ttf-dejavu-sans-mono-2.37-hab24e00_0.tar.bz2#0c96522c6bdaed4b1566d11387caaf45 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bio/last/lastdb/environment.linux-64.pin.txt | 7 +++---- bio/last/lastdb/environment.yaml | 2 +- 2 files changed, 4 insertions(+), 5 deletions(-) diff --git a/bio/last/lastdb/environment.linux-64.pin.txt b/bio/last/lastdb/environment.linux-64.pin.txt index fb563b49100..e2532d4d899 100644 --- a/bio/last/lastdb/environment.linux-64.pin.txt +++ b/bio/last/lastdb/environment.linux-64.pin.txt @@ -5,7 +5,7 @@ https://conda.anaconda.org/conda-forge/linux-64/_libgcc_mutex-0.1-conda_forge.tar.bz2#d7c89558ba9fa0495403155b64376d81 https://conda.anaconda.org/conda-forge/linux-64/ca-certificates-2024.7.4-hbcca054_0.conda#23ab7665c5f63cfb9f1f6195256daac6 https://conda.anaconda.org/conda-forge/linux-64/ld_impl_linux-64-2.40-hf3520f5_7.conda#b80f2f396ca2c28b8c14c437a4ed1e74 -https://conda.anaconda.org/conda-forge/linux-64/python_abi-3.12-4_cp312.conda#dccc2d142812964fcc6abdc97b672dff +https://conda.anaconda.org/conda-forge/linux-64/python_abi-3.12-5_cp312.conda#0424ae29b104430108f5218a66db7260 https://conda.anaconda.org/conda-forge/noarch/tzdata-2024a-h0c530f3_0.conda#161081fc7cec0bfda0d86d7cb595f8d8 https://conda.anaconda.org/conda-forge/linux-64/libgomp-14.1.0-h77fa898_0.conda#ae061a5ed5f05818acdf9adab72c146d https://conda.anaconda.org/conda-forge/linux-64/_openmp_mutex-4.5-2_gnu.tar.bz2#73aaf86a425cc6e73fcf236a5a46396d @@ -34,7 +34,6 @@ https://conda.anaconda.org/conda-forge/linux-64/libxcb-1.16-hd590300_0.conda#151 https://conda.anaconda.org/conda-forge/linux-64/perl-5.32.1-7_hd590300_perl5.conda#f2cfec9406850991f4e3d960cc9e3321 https://conda.anaconda.org/conda-forge/linux-64/readline-8.2-h8228510_1.conda#47d31b792659ce70f470b5c82fdfb7a4 https://conda.anaconda.org/conda-forge/linux-64/tk-8.6.13-noxft_h4845f30_101.conda#d453b98d9c83e71da0741bb0ff4d76bc -https://conda.anaconda.org/conda-forge/linux-64/zlib-1.3.1-h4ab18f5_1.conda#9653f1bf3766164d0e65fa723cabbc54 https://conda.anaconda.org/conda-forge/linux-64/zstd-1.5.6-ha6fb4c9_0.conda#4d056880988120e29d75bfff282e0f45 https://conda.anaconda.org/conda-forge/linux-64/freetype-2.12.1-h267a509_2.conda#9ae35c3d96db2c94ce0cef86efdfa2cb https://conda.anaconda.org/conda-forge/linux-64/libtiff-4.6.0-h46a8edc_4.conda#a7e3a62981350e232e0e7345b5aea580 @@ -42,8 +41,8 @@ https://conda.anaconda.org/conda-forge/linux-64/parallel-20240722-ha770c72_0.con https://conda.anaconda.org/conda-forge/linux-64/python-3.12.5-h2ad013b_0_cpython.conda#9c56c4df45f6571b13111d8df2448692 https://conda.anaconda.org/conda-forge/linux-64/lcms2-2.16-hb7c19ff_0.conda#51bb7010fc86f70eee639b4bb7a894f5 https://conda.anaconda.org/conda-forge/linux-64/openjpeg-2.5.2-h488ebb8_0.conda#7f2e286780f072ed750df46dc2631138 -https://conda.anaconda.org/conda-forge/noarch/setuptools-72.1.0-pyhd8ed1ab_0.conda#e06d4c26df4f958a8d38696f2c344d15 +https://conda.anaconda.org/conda-forge/noarch/setuptools-72.2.0-pyhd8ed1ab_0.conda#1462aa8b243aad09ef5d0841c745eb89 https://conda.anaconda.org/conda-forge/noarch/wheel-0.44.0-pyhd8ed1ab_0.conda#d44e3b085abcaef02983c6305b84b584 https://conda.anaconda.org/conda-forge/linux-64/pillow-10.4.0-py312h287a98d_0.conda#59ea71eed98aee0bebbbdd3b118167c7 https://conda.anaconda.org/conda-forge/noarch/pip-24.2-pyhd8ed1ab_0.conda#6721aef6bfe5937abe70181545dd2c51 -https://conda.anaconda.org/bioconda/linux-64/last-1550-h43eeafb_0.tar.bz2#ee6566f27bbf9c35413359a8007d37ff +https://conda.anaconda.org/bioconda/linux-64/last-1571-h43eeafb_0.tar.bz2#37196ba9aed615c5aa2a298e9d8adbd8 diff --git a/bio/last/lastdb/environment.yaml b/bio/last/lastdb/environment.yaml index 3cd69035c86..81144a4d927 100644 --- a/bio/last/lastdb/environment.yaml +++ b/bio/last/lastdb/environment.yaml @@ -3,4 +3,4 @@ channels: - bioconda - nodefaults dependencies: - - last =1550 + - last =1571 From 2c1332948b3082438fd2021087592b47a48c8a5c Mon Sep 17 00:00:00 2001 From: "snakedeploy-bot[bot]" <115615832+snakedeploy-bot[bot]@users.noreply.github.com> Date: Fri, 23 Aug 2024 03:40:38 +0000 Subject: [PATCH 58/62] perf: autobump bio/last/lastal (#3131) Automatic bump of bio/last/lastal. --------- Co-authored-by: snakedeploy-bot[bot] <115615832+snakedeploy-bot[bot]@users.noreply.github.com> --- bio/last/lastal/environment.linux-64.pin.txt | 7 +++---- bio/last/lastal/environment.yaml | 2 +- 2 files changed, 4 insertions(+), 5 deletions(-) diff --git a/bio/last/lastal/environment.linux-64.pin.txt b/bio/last/lastal/environment.linux-64.pin.txt index fb563b49100..e2532d4d899 100644 --- a/bio/last/lastal/environment.linux-64.pin.txt +++ b/bio/last/lastal/environment.linux-64.pin.txt @@ -5,7 +5,7 @@ https://conda.anaconda.org/conda-forge/linux-64/_libgcc_mutex-0.1-conda_forge.tar.bz2#d7c89558ba9fa0495403155b64376d81 https://conda.anaconda.org/conda-forge/linux-64/ca-certificates-2024.7.4-hbcca054_0.conda#23ab7665c5f63cfb9f1f6195256daac6 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https://conda.anaconda.org/conda-forge/linux-64/readline-8.2-h8228510_1.conda#47d31b792659ce70f470b5c82fdfb7a4 https://conda.anaconda.org/conda-forge/linux-64/tk-8.6.13-noxft_h4845f30_101.conda#d453b98d9c83e71da0741bb0ff4d76bc -https://conda.anaconda.org/conda-forge/linux-64/zlib-1.3.1-h4ab18f5_1.conda#9653f1bf3766164d0e65fa723cabbc54 https://conda.anaconda.org/conda-forge/linux-64/zstd-1.5.6-ha6fb4c9_0.conda#4d056880988120e29d75bfff282e0f45 https://conda.anaconda.org/conda-forge/linux-64/freetype-2.12.1-h267a509_2.conda#9ae35c3d96db2c94ce0cef86efdfa2cb https://conda.anaconda.org/conda-forge/linux-64/libtiff-4.6.0-h46a8edc_4.conda#a7e3a62981350e232e0e7345b5aea580 @@ -42,8 +41,8 @@ https://conda.anaconda.org/conda-forge/linux-64/parallel-20240722-ha770c72_0.con https://conda.anaconda.org/conda-forge/linux-64/python-3.12.5-h2ad013b_0_cpython.conda#9c56c4df45f6571b13111d8df2448692 https://conda.anaconda.org/conda-forge/linux-64/lcms2-2.16-hb7c19ff_0.conda#51bb7010fc86f70eee639b4bb7a894f5 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3cd69035c86..81144a4d927 100644 --- a/bio/last/lastal/environment.yaml +++ b/bio/last/lastal/environment.yaml @@ -3,4 +3,4 @@ channels: - bioconda - nodefaults dependencies: - - last =1550 + - last =1571 From b5bb55238100f1f4c520d173323ce4c84e035cbb Mon Sep 17 00:00:00 2001 From: "snakedeploy-bot[bot]" <115615832+snakedeploy-bot[bot]@users.noreply.github.com> Date: Fri, 23 Aug 2024 03:53:56 +0000 Subject: [PATCH 59/62] perf: autobump bio/multiqc (#3132) Automatic bump of bio/multiqc. --------- Co-authored-by: snakedeploy-bot[bot] <115615832+snakedeploy-bot[bot]@users.noreply.github.com> --- bio/multiqc/environment.linux-64.pin.txt | 59 ++++++++++++------------ bio/multiqc/environment.yaml | 2 +- 2 files changed, 30 insertions(+), 31 deletions(-) diff --git a/bio/multiqc/environment.linux-64.pin.txt b/bio/multiqc/environment.linux-64.pin.txt index 0c18d3e787b..cac5dfbc956 100644 --- a/bio/multiqc/environment.linux-64.pin.txt +++ b/bio/multiqc/environment.linux-64.pin.txt @@ -10,14 +10,14 @@ https://conda.anaconda.org/conda-forge/noarch/font-ttf-source-code-pro-2.038-h77 https://conda.anaconda.org/conda-forge/noarch/font-ttf-ubuntu-0.83-h77eed37_2.conda#cbbe59391138ea5ad3658c76912e147f https://conda.anaconda.org/conda-forge/linux-64/ld_impl_linux-64-2.40-hf3520f5_7.conda#b80f2f396ca2c28b8c14c437a4ed1e74 https://conda.anaconda.org/conda-forge/linux-64/mathjax-2.7.7-ha770c72_3.tar.bz2#86e69bd82c2a2c6fd29f5ab7e02b3691 -https://conda.anaconda.org/conda-forge/linux-64/python_abi-3.11-4_cp311.conda#d786502c97404c94d7d58d258a445a65 +https://conda.anaconda.org/conda-forge/linux-64/python_abi-3.12-5_cp312.conda#0424ae29b104430108f5218a66db7260 https://conda.anaconda.org/conda-forge/noarch/tzdata-2024a-h0c530f3_0.conda#161081fc7cec0bfda0d86d7cb595f8d8 https://conda.anaconda.org/conda-forge/noarch/fonts-conda-forge-1-0.tar.bz2#f766549260d6815b0c52253f1fb1bb29 https://conda.anaconda.org/conda-forge/linux-64/libgomp-14.1.0-h77fa898_0.conda#ae061a5ed5f05818acdf9adab72c146d https://conda.anaconda.org/conda-forge/linux-64/_openmp_mutex-4.5-2_gnu.tar.bz2#73aaf86a425cc6e73fcf236a5a46396d https://conda.anaconda.org/conda-forge/linux-64/libgcc-ng-14.1.0-h77fa898_0.conda#ca0fad6a41ddaef54a153b78eccb5037 -https://conda.anaconda.org/conda-forge/linux-64/bzip2-1.0.8-hd590300_5.conda#69b8b6202a07720f448be700e300ccf4 -https://conda.anaconda.org/conda-forge/linux-64/libdeflate-1.20-hd590300_0.conda#8e88f9389f1165d7c0936fe40d9a9a79 +https://conda.anaconda.org/conda-forge/linux-64/bzip2-1.0.8-h4bc722e_7.conda#62ee74e96c5ebb0af99386de58cf9553 +https://conda.anaconda.org/conda-forge/linux-64/libdeflate-1.21-h4bc722e_0.conda#36ce76665bf67f5aac36be7a0d21b7f3 https://conda.anaconda.org/conda-forge/linux-64/libexpat-2.6.2-h59595ed_0.conda#e7ba12deb7020dd080c6c70e7b6f6a3d https://conda.anaconda.org/conda-forge/linux-64/libffi-3.4.2-h7f98852_5.tar.bz2#d645c6d2ac96843a2bfaccd2d62b3ac3 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https://conda.anaconda.org/conda-forge/linux-64/xorg-libxau-1.0.11-hd590300_0.conda#2c80dc38fface310c9bd81b17037fee5 https://conda.anaconda.org/conda-forge/linux-64/xorg-libxdmcp-1.1.3-h7f98852_0.tar.bz2#be93aabceefa2fac576e971aef407908 @@ -47,11 +47,11 @@ https://conda.anaconda.org/conda-forge/linux-64/tk-8.6.13-noxft_h4845f30_101.con https://conda.anaconda.org/conda-forge/linux-64/zstd-1.5.6-ha6fb4c9_0.conda#4d056880988120e29d75bfff282e0f45 https://conda.anaconda.org/conda-forge/linux-64/freetype-2.12.1-h267a509_2.conda#9ae35c3d96db2c94ce0cef86efdfa2cb https://conda.anaconda.org/conda-forge/linux-64/libopenblas-0.3.27-pthreads_hac2b453_1.conda#ae05ece66d3924ac3d48b4aa3fa96cec -https://conda.anaconda.org/conda-forge/linux-64/libtiff-4.6.0-h1dd3fc0_3.conda#66f03896ffbe1a110ffda05c7a856504 -https://conda.anaconda.org/conda-forge/linux-64/nss-3.102-h593d115_0.conda#40e5e48c55a45621c4399ca9236406b7 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-https://conda.anaconda.org/bioconda/noarch/multiqc-1.23-pyhdfd78af_0.tar.bz2#362593cad7b0758ca698ee61acb85803 +https://conda.anaconda.org/bioconda/noarch/multiqc-1.24.1-pyhdfd78af_0.tar.bz2#9d85bb8d72c99ef99bb9806fd879c985 diff --git a/bio/multiqc/environment.yaml b/bio/multiqc/environment.yaml index b0d1ddd9d85..83e4a3cb3ca 100644 --- a/bio/multiqc/environment.yaml +++ b/bio/multiqc/environment.yaml @@ -3,5 +3,5 @@ channels: - bioconda - nodefaults dependencies: - - multiqc =1.23 + - multiqc =1.24.1 - snakemake-wrapper-utils =0.6.2 From 065d45eba68db3375213095ecf2332705b333cf0 Mon Sep 17 00:00:00 2001 From: "snakedeploy-bot[bot]" <115615832+snakedeploy-bot[bot]@users.noreply.github.com> Date: Fri, 23 Aug 2024 04:54:35 +0000 Subject: [PATCH 60/62] perf: autobump bio/reference/ensembl-mysql-table (#3133) Automatic bump of bio/reference/ensembl-mysql-table. ## Summary by CodeRabbit - **New Features** - Updated package dependencies to ensure compatibility and stability, potentially introducing new features and bug fixes. - **Bug Fixes** - Enhanced compatibility with newer versions of R packages, which may improve the behavior of related applications and scripts. - **Chores** - Regular maintenance updates to keep the environment aligned with the latest stable releases of dependencies. --------- Co-authored-by: snakedeploy-bot[bot] <115615832+snakedeploy-bot[bot]@users.noreply.github.com> --- .../environment.linux-64.pin.txt | 52 +++++++++---------- .../ensembl-mysql-table/environment.yaml | 8 +-- 2 files changed, 30 insertions(+), 30 deletions(-) diff --git a/bio/reference/ensembl-mysql-table/environment.linux-64.pin.txt b/bio/reference/ensembl-mysql-table/environment.linux-64.pin.txt index e82b3f7e2ad..24a6aa4d0aa 100644 --- a/bio/reference/ensembl-mysql-table/environment.linux-64.pin.txt +++ b/bio/reference/ensembl-mysql-table/environment.linux-64.pin.txt @@ -13,7 +13,7 @@ https://conda.anaconda.org/conda-forge/noarch/font-ttf-ubuntu-0.83-h77eed37_2.co 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https://conda.anaconda.org/conda-forge/linux-64/r-bit64-4.0.5-r43hb1dbf0f_3.conda#0497d0061211b14cb89186a43d132ad1 https://conda.anaconda.org/conda-forge/linux-64/r-cachem-1.1.0-r43hb1dbf0f_1.conda#02b195910b59c2cfd1fb7159edbb047a @@ -156,7 +156,7 @@ https://conda.anaconda.org/conda-forge/linux-64/r-processx-3.8.4-r43hb1dbf0f_1.c https://conda.anaconda.org/conda-forge/linux-64/r-timechange-0.3.0-r43ha18555a_1.conda#da155dc726414cca04cdc76a297c4463 https://conda.anaconda.org/conda-forge/noarch/r-tinytex-0.52-r43hc72bb7e_0.conda#b60613abdfd0690e8b4ed8dfb142511f https://conda.anaconda.org/conda-forge/linux-64/r-tzdb-0.4.0-r43ha18555a_2.conda#af670d1acc46c7aa0973ad190e0f52a0 -https://conda.anaconda.org/conda-forge/linux-64/r-xml2-1.3.6-r43hbfba7a4_1.conda#545f26a602ff99102e7fd70f425ead32 +https://conda.anaconda.org/conda-forge/linux-64/r-xml2-1.3.6-r43h8194278_2.conda#bf45fca038138a632e44be28adad50b5 https://conda.anaconda.org/conda-forge/noarch/r-callr-3.7.6-r43hc72bb7e_1.conda#cb327fa8f604dce0de71143459185b9f https://conda.anaconda.org/conda-forge/noarch/r-gtable-0.3.5-r43hc72bb7e_1.conda#373d1655e4d3c45b6abe455d8a52b14e https://conda.anaconda.org/conda-forge/linux-64/r-htmltools-0.5.8.1-r43ha18555a_1.conda#7b26688542e1b7a39fc62affeef9d32e @@ -164,7 +164,7 @@ https://conda.anaconda.org/conda-forge/noarch/r-knitr-1.48-r43hc72bb7e_0.conda#7 https://conda.anaconda.org/conda-forge/linux-64/r-lubridate-1.9.3-r43hdb488b9_1.conda#7bce2af86e6010576bdb4718cbd985b9 https://conda.anaconda.org/conda-forge/noarch/r-memoise-2.0.1-r43hc72bb7e_3.conda#98e3d2eb6635a5f7b8af487f47184a98 https://conda.anaconda.org/conda-forge/linux-64/r-mgcv-1.9_1-r43h0d28552_1.conda#154d840fb734a3f80a5ef623b52ff6cd -https://conda.anaconda.org/conda-forge/linux-64/r-openssl-2.2.0-r43h5bbf899_1.conda#d0d7032f575c8ed6ae83cd8c4d7214e4 +https://conda.anaconda.org/conda-forge/linux-64/r-openssl-2.2.1-r43h5bbf899_0.conda#5c47f4efe6393dff5a3eb661c24cb589 https://conda.anaconda.org/conda-forge/noarch/r-scales-1.3.0-r43hc72bb7e_1.conda#119d9c10dc652ac1492fc49951d86860 https://conda.anaconda.org/conda-forge/linux-64/r-systemfonts-1.1.0-r43h38d38ca_1.conda#03e51a887e5284ddae8ea6983e682e76 https://conda.anaconda.org/conda-forge/linux-64/r-vctrs-0.6.5-r43h0d4f4ea_1.conda#7f4c30bb576acec2a682c40790c2d406 @@ -181,7 +181,7 @@ https://conda.anaconda.org/conda-forge/linux-64/r-sass-0.4.9-r43ha18555a_1.conda https://conda.anaconda.org/conda-forge/noarch/r-stringr-1.5.1-r43h785f33e_1.conda#b997c27a396a991db9fba6ad9c07da40 https://conda.anaconda.org/conda-forge/linux-64/r-textshaping-0.4.0-r43ha47bcaa_2.conda#31795e19cf2b2e5b7cef1dc0f0852638 https://conda.anaconda.org/conda-forge/noarch/r-tidyselect-1.2.1-r43hc72bb7e_1.conda#f55367f874307bb57575ac1506079178 -https://conda.anaconda.org/conda-forge/noarch/r-bslib-0.7.0-r43hc72bb7e_1.conda#eaccfd4ea4612eb224991c3a4af32349 +https://conda.anaconda.org/conda-forge/noarch/r-bslib-0.8.0-r43hc72bb7e_0.conda#1ad48e7ec3071fd043d89ce5f8c9eb7d https://conda.anaconda.org/conda-forge/noarch/r-gargle-1.5.2-r43h785f33e_1.conda#9b055b60f2d36aa2a991840f20be6f07 https://conda.anaconda.org/conda-forge/noarch/r-progress-1.2.3-r43hc72bb7e_1.conda#e50711aa4ed08fae208148998c92f296 https://conda.anaconda.org/conda-forge/linux-64/r-ragg-1.3.2-r43h6bbb899_1.conda#b4f414533aa947b54275f1c8be45dcd4 @@ -194,10 +194,10 @@ https://conda.anaconda.org/conda-forge/noarch/r-forcats-1.0.0-r43hc72bb7e_2.cond https://conda.anaconda.org/conda-forge/noarch/r-ggplot2-3.5.1-r43hc72bb7e_1.conda#a828d1513cabc43cf0711ee0eaec53b2 https://conda.anaconda.org/conda-forge/noarch/r-googledrive-2.1.1-r43hc72bb7e_2.conda#25f614d432724c7a673859b804ec9537 https://conda.anaconda.org/conda-forge/noarch/r-rematch2-2.1.2-r43hc72bb7e_4.conda#3a4a5f3929460a3e8450d94aac2d85c2 -https://conda.anaconda.org/conda-forge/noarch/r-rmarkdown-2.27-r43hc72bb7e_1.conda#4b681e35650d7d10737bc0c6ed80ae9a -https://conda.anaconda.org/conda-forge/noarch/r-rvest-1.0.4-r43hc72bb7e_0.conda#01ff5b7fd4bfafd75c0b91e6d3a1d443 +https://conda.anaconda.org/conda-forge/noarch/r-rmarkdown-2.28-r43hc72bb7e_0.conda#93294aae24898657d02e71733af00436 +https://conda.anaconda.org/conda-forge/noarch/r-rvest-1.0.4-r43hc72bb7e_1.conda#f9ba3380ae759d5e7e6fd3479d648795 https://conda.anaconda.org/conda-forge/linux-64/r-vroom-1.6.5-r43h0d4f4ea_1.conda#2fc1d56664063aaa4ffd43a702a71baf -https://conda.anaconda.org/conda-forge/noarch/r-dtplyr-1.3.1-r43hc72bb7e_1.conda#85ba0e234af279259478526f5cdf952f +https://conda.anaconda.org/conda-forge/noarch/r-dtplyr-1.3.1-r43hc72bb7e_2.conda#1de89f4b9a7560db5ed812ee4e92879b https://conda.anaconda.org/conda-forge/noarch/r-googlesheets4-1.1.1-r43h785f33e_2.conda#332576dbba1cf5eea98ade568264a297 https://conda.anaconda.org/conda-forge/linux-64/r-readr-2.1.5-r43h0d4f4ea_1.conda#e3ffadf38171b07d753f0bb4f744d73f https://conda.anaconda.org/conda-forge/linux-64/r-readxl-1.4.3-r43he58e087_1.conda#32e15ee3765d83331fd41f55fdc509ae @@ -207,4 +207,4 @@ https://conda.anaconda.org/conda-forge/noarch/r-broom-1.0.6-r43hc72bb7e_1.conda# https://conda.anaconda.org/conda-forge/noarch/r-dbplyr-2.5.0-r43hc72bb7e_1.conda#73cd48c8632ca1a98381cc0f1ebed3d4 https://conda.anaconda.org/conda-forge/linux-64/r-haven-2.5.4-r43h0d4f4ea_1.conda#5ea73f6c0626a144907ac2748d19050e https://conda.anaconda.org/conda-forge/noarch/r-modelr-0.1.11-r43hc72bb7e_2.conda#2cdd8c74b0c949695af0debfd3a44974 -https://conda.anaconda.org/conda-forge/noarch/r-tidyverse-2.0.0-r43h785f33e_1.conda#390310ae8a44cbd35c8d27f5efa362cb +https://conda.anaconda.org/conda-forge/noarch/r-tidyverse-2.0.0-r43h785f33e_2.conda#02a988567686de86cc822fb4e33b14ad diff --git a/bio/reference/ensembl-mysql-table/environment.yaml b/bio/reference/ensembl-mysql-table/environment.yaml index acb35ffbf0a..c5b07b89136 100644 --- a/bio/reference/ensembl-mysql-table/environment.yaml +++ b/bio/reference/ensembl-mysql-table/environment.yaml @@ -3,7 +3,7 @@ channels: - bioconda - nodefaults dependencies: - - r-nanoparquet =0.3 - - r-tidyverse =2.0 - - r-dbplyr =2.5 - - r-rmariadb =1.2 + - r-nanoparquet =0.3.1 + - r-tidyverse =2.0.0 + - r-dbplyr =2.5.0 + - r-rmariadb =1.2.2 From 8563e882e61ddad7db6386f65803d13a6c1926af Mon Sep 17 00:00:00 2001 From: tdayris Date: Fri, 23 Aug 2024 13:20:00 +0200 Subject: [PATCH 61/62] feat: Pcaexplorer pcaplot (#1728) MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit ### Description This PR adds a wrapper for [pcaExplorer](https://www.bioconductor.org/packages/release/bioc/vignettes/pcaExplorer/inst/doc/pcaExplorer.html#pcaExplorer_User_Guide)'s `pcaplot` function. ### QC * [X] I confirm that: For all wrappers added by this PR, * there is a test case which covers any introduced changes, * `input:` and `output:` file paths in the resulting rule can be changed arbitrarily, * either the wrapper can only use a single core, or the example rule contains a `threads: x` statement with `x` being a reasonable default, * rule names in the test case are in [snake_case](https://en.wikipedia.org/wiki/Snake_case) and somehow tell what the rule is about or match the tools purpose or name (e.g., `map_reads` for a step that maps reads), * all `environment.yaml` specifications follow [the respective best practices](https://stackoverflow.com/a/64594513/2352071), * wherever possible, command line arguments are inferred and set automatically (e.g. based on file extensions in `input:` or `output:`), * all fields of the example rules in the `Snakefile`s and their entries are explained via comments (`input:`/`output:`/`params:` etc.), * `stderr` and/or `stdout` are logged correctly (`log:`), depending on the wrapped tool, * temporary files are either written to a unique hidden folder in the working directory, or (better) stored where the Python function `tempfile.gettempdir()` points to (see [here](https://docs.python.org/3/library/tempfile.html#tempfile.gettempdir); this also means that using any Python `tempfile` default behavior works), * the `meta.yaml` contains a link to the documentation of the respective tool or command, * `Snakefile`s pass the linting (`snakemake --lint`), * `Snakefile`s are formatted with [snakefmt](https://github.com/snakemake/snakefmt), * Python wrapper scripts are formatted with [black](https://black.readthedocs.io). * Conda environments use a minimal amount of channels, in recommended ordering. E.g. for bioconda, use (conda-forge, bioconda, nodefaults, as conda-forge should have highest priority and defaults channels are usually not needed because most packages are in conda-forge nowadays). ## Summary by CodeRabbit - **New Features** - Introduced environment specification files (`environment.linux-64.pin.txt` and `environment.yaml`) for easier setup of computational environments. - Added a `meta.yaml` configuration for the PCA-Explorer PCA-plot tool, enhancing visualization capabilities for PCA results. - Implemented a `Snakefile` for automating PCA plotting processes, improving reproducibility in data analysis workflows. - Launched a wrapper R script to streamline execution of PCA analysis within Snakemake workflows. - **Tests** - Added a new test function to validate PCA plotting functionality within the testing suite. --------- Co-authored-by: tdayris Co-authored-by: tdayris Co-authored-by: Johannes Köster Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> Co-authored-by: snakedeploy-bot[bot] <115615832+snakedeploy-bot[bot]@users.noreply.github.com> Co-authored-by: Felix Mölder Co-authored-by: Christopher Schröder Co-authored-by: Filipe G. Vieira <1151762+fgvieira@users.noreply.github.com> --- .../pcaplot/environment.linux-64.pin.txt | 313 ++++++++++++++++++ bio/pcaexplorer/pcaplot/environment.yaml | 6 + bio/pcaexplorer/pcaplot/meta.yaml | 13 + bio/pcaexplorer/pcaplot/test/Snakefile | 13 + bio/pcaexplorer/pcaplot/test/dst.RDS | Bin 0 -> 180608 bytes bio/pcaexplorer/pcaplot/wrapper.R | 69 ++++ test.py | 8 + 7 files changed, 422 insertions(+) create mode 100644 bio/pcaexplorer/pcaplot/environment.linux-64.pin.txt create mode 100644 bio/pcaexplorer/pcaplot/environment.yaml create mode 100644 bio/pcaexplorer/pcaplot/meta.yaml create mode 100644 bio/pcaexplorer/pcaplot/test/Snakefile create mode 100644 bio/pcaexplorer/pcaplot/test/dst.RDS create mode 100644 bio/pcaexplorer/pcaplot/wrapper.R diff --git a/bio/pcaexplorer/pcaplot/environment.linux-64.pin.txt b/bio/pcaexplorer/pcaplot/environment.linux-64.pin.txt new file mode 100644 index 00000000000..7869479af66 --- /dev/null +++ b/bio/pcaexplorer/pcaplot/environment.linux-64.pin.txt @@ -0,0 +1,313 @@ +# This file may be used to create an environment using: +# $ conda create --name --file +# platform: linux-64 +@EXPLICIT +https://conda.anaconda.org/conda-forge/linux-64/_libgcc_mutex-0.1-conda_forge.tar.bz2#d7c89558ba9fa0495403155b64376d81 +https://conda.anaconda.org/conda-forge/noarch/_r-mutex-1.0.1-anacondar_1.tar.bz2#19f9db5f4f1b7f5ef5f6d67207f25f38 +https://conda.anaconda.org/conda-forge/noarch/_sysroot_linux-64_curr_repodata_hack-3-h69a702a_16.conda#1c005af0c6ff22814b7c52ee448d4bea +https://conda.anaconda.org/conda-forge/linux-64/ca-certificates-2024.7.4-hbcca054_0.conda#23ab7665c5f63cfb9f1f6195256daac6 +https://conda.anaconda.org/conda-forge/noarch/font-ttf-dejavu-sans-mono-2.37-hab24e00_0.tar.bz2#0c96522c6bdaed4b1566d11387caaf45 +https://conda.anaconda.org/conda-forge/noarch/font-ttf-inconsolata-3.000-h77eed37_0.tar.bz2#34893075a5c9e55cdafac56607368fc6 +https://conda.anaconda.org/conda-forge/noarch/font-ttf-source-code-pro-2.038-h77eed37_0.tar.bz2#4d59c254e01d9cde7957100457e2d5fb +https://conda.anaconda.org/conda-forge/noarch/font-ttf-ubuntu-0.83-h77eed37_2.conda#cbbe59391138ea5ad3658c76912e147f +https://conda.anaconda.org/conda-forge/linux-64/ld_impl_linux-64-2.40-hf3520f5_7.conda#b80f2f396ca2c28b8c14c437a4ed1e74 +https://conda.anaconda.org/conda-forge/noarch/libgcc-devel_linux-64-14.1.0-h5d3d1c9_100.conda#6d4f65dc440f7b3422113b135be19703 +https://conda.anaconda.org/conda-forge/noarch/libstdcxx-devel_linux-64-14.1.0-h5d3d1c9_100.conda#cedc62fd8c4cf28f23d3cd5db7839e99 +https://conda.anaconda.org/conda-forge/linux-64/pandoc-3.2.1-ha770c72_0.conda#b39b12d3809e4042f832b76192e0e7e8 +https://conda.anaconda.org/conda-forge/linux-64/python_abi-3.12-4_cp312.conda#dccc2d142812964fcc6abdc97b672dff +https://conda.anaconda.org/conda-forge/noarch/tzdata-2024a-h0c530f3_0.conda#161081fc7cec0bfda0d86d7cb595f8d8 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100644 index 00000000000..7c0fad3bebb --- /dev/null +++ b/bio/pcaexplorer/pcaplot/environment.yaml @@ -0,0 +1,6 @@ +channels: + - conda-forge + - bioconda + - nodefaults +dependencies: + - bioconductor-pcaexplorer=2.28.0 \ No newline at end of file diff --git a/bio/pcaexplorer/pcaplot/meta.yaml b/bio/pcaexplorer/pcaplot/meta.yaml new file mode 100644 index 00000000000..0e6e66497e7 --- /dev/null +++ b/bio/pcaexplorer/pcaplot/meta.yaml @@ -0,0 +1,13 @@ +name: "PCA-Explorer PCA-plot" +description: Plots the results of PCA on a 2-dimensional space +url: https://www.bioconductor.org/packages/release/bioc/vignettes/pcaExplorer/inst/doc/pcaExplorer.html#91_pcaplot +authors: + - Thibault Dayris +input: + - Path to DESeqTransform object, such as rlog or vst transformed data +output: + - Path to PCA plot (SVG formatted) +params: + - extra: Optional parameters, besides `x`. +notes: | + This tool does not handle multi threading. diff --git a/bio/pcaexplorer/pcaplot/test/Snakefile 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([8563e88](https://www.github.com/snakemake/snakemake-wrappers/commit/8563e882e61ddad7db6386f65803d13a6c1926af)) ### Performance Improvements * autobump bio/bbtools ([#3127](https://www.github.com/snakemake/snakemake-wrappers/issues/3127)) ([a9bd6df](https://www.github.com/snakemake/snakemake-wrappers/commit/a9bd6dfdeee5692c76507148e12e81547c0c0906)) * autobump bio/gatk3/printreads ([#3129](https://www.github.com/snakemake/snakemake-wrappers/issues/3129)) ([97b2c9d](https://www.github.com/snakemake/snakemake-wrappers/commit/97b2c9d218b120cda5991303f7b1b3d5b854bf2f)) * autobump bio/last/lastal ([#3131](https://www.github.com/snakemake/snakemake-wrappers/issues/3131)) ([2c13329](https://www.github.com/snakemake/snakemake-wrappers/commit/2c1332948b3082438fd2021087592b47a48c8a5c)) * autobump bio/last/lastdb ([#3130](https://www.github.com/snakemake/snakemake-wrappers/issues/3130)) ([ce9dfd4](https://www.github.com/snakemake/snakemake-wrappers/commit/ce9dfd459862a86fa0cb960708e232d21894bd60)) * autobump bio/multiqc ([#3132](https://www.github.com/snakemake/snakemake-wrappers/issues/3132)) ([b5bb552](https://www.github.com/snakemake/snakemake-wrappers/commit/b5bb55238100f1f4c520d173323ce4c84e035cbb)) * autobump bio/reference/ensembl-mysql-table ([#3133](https://www.github.com/snakemake/snakemake-wrappers/issues/3133)) ([065d45e](https://www.github.com/snakemake/snakemake-wrappers/commit/065d45eba68db3375213095ecf2332705b333cf0)) --- This PR was generated with [Release Please](https://github.com/googleapis/release-please). See [documentation](https://github.com/googleapis/release-please#release-please). Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> --- CHANGELOG.md | 17 +++++++++++++++++ 1 file changed, 17 insertions(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index fff71d9e785..5a88c8ee5bd 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -1,5 +1,22 @@ # Changelog +## [4.2.0](https://www.github.com/snakemake/snakemake-wrappers/compare/v4.1.1...v4.2.0) (2024-08-23) + + +### Features + +* Pcaexplorer pcaplot ([#1728](https://www.github.com/snakemake/snakemake-wrappers/issues/1728)) ([8563e88](https://www.github.com/snakemake/snakemake-wrappers/commit/8563e882e61ddad7db6386f65803d13a6c1926af)) + + +### Performance Improvements + +* autobump bio/bbtools ([#3127](https://www.github.com/snakemake/snakemake-wrappers/issues/3127)) ([a9bd6df](https://www.github.com/snakemake/snakemake-wrappers/commit/a9bd6dfdeee5692c76507148e12e81547c0c0906)) +* autobump bio/gatk3/printreads ([#3129](https://www.github.com/snakemake/snakemake-wrappers/issues/3129)) ([97b2c9d](https://www.github.com/snakemake/snakemake-wrappers/commit/97b2c9d218b120cda5991303f7b1b3d5b854bf2f)) +* autobump bio/last/lastal ([#3131](https://www.github.com/snakemake/snakemake-wrappers/issues/3131)) ([2c13329](https://www.github.com/snakemake/snakemake-wrappers/commit/2c1332948b3082438fd2021087592b47a48c8a5c)) +* autobump bio/last/lastdb ([#3130](https://www.github.com/snakemake/snakemake-wrappers/issues/3130)) ([ce9dfd4](https://www.github.com/snakemake/snakemake-wrappers/commit/ce9dfd459862a86fa0cb960708e232d21894bd60)) +* autobump bio/multiqc ([#3132](https://www.github.com/snakemake/snakemake-wrappers/issues/3132)) ([b5bb552](https://www.github.com/snakemake/snakemake-wrappers/commit/b5bb55238100f1f4c520d173323ce4c84e035cbb)) +* autobump bio/reference/ensembl-mysql-table ([#3133](https://www.github.com/snakemake/snakemake-wrappers/issues/3133)) ([065d45e](https://www.github.com/snakemake/snakemake-wrappers/commit/065d45eba68db3375213095ecf2332705b333cf0)) + ### [4.1.1](https://www.github.com/snakemake/snakemake-wrappers/compare/v4.1.0...v4.1.1) (2024-08-21)