Genoflu (#53750)

* Update varfish-cli to 0.7.0 (#53454)

* update package version and dependencies for ViroConstrictor 1.5.0 (#53456)

* Disable mac builds for pyopenms again (#53396)

* Update meta.yaml

* Update ICU dependency version range

* Update meta.yaml

* Update recipes/pyopenms/meta.yaml

Co-authored-by: Martin Grigorov <[email protected]>

* Bump build number to 4

* Skip build on OSX and increment version

---------

Co-authored-by: Martin Grigorov <[email protected]>

* Add missing dependencies for CAT_pack reads (#53459)

* Update bakta to 1.10.4 (#53461)

* Update piscem to 0.12.0 (#53439)

* Update piscem to 0.12.0

* Update conda_build_config.yaml

* Update meta.yaml

---------

Co-authored-by: Rob Patro <[email protected]>

* gdc-client: remove pyopenssl pin (#53463)

* Update mgnify-pipelines-toolkit to 0.2.0 (#53464)

* Update rbpbench to 1.0.2 (#53466)

* Update strangepg to 0.8.18 (#53462)

* Update solvebio to 2.30.0 (#53467)

* Update autobigs-engine to 0.8.0 (#53469)

* Update notramp to 1.1.8 (#53465)

* seismic-rna: add aarch64/arm64 builds (#53423)

Signed-off-by: Martin Tzvetanov Grigorov <[email protected]>

* Update paraphase to 3.1.2 (#53471)

* Add nbitk to bioconda (#53460)

* Update grepq to 1.4.2 (#53472)

* Add autobigs-cli (#53470)

* Update diamond to 2.1.11 (#53473)

* Update flexynesis to 0.2.14 (#53478)

* Update paraphase to 3.2.0 (#53479)

* Update pybarrnap to 0.5.1 (#53476)

* Update pybarrnap to 0.5.1

* Update meta.yaml

---------

Co-authored-by: Joshua Zhuang <[email protected]>

* Update simpleaf to 0.19.0 (#53475)

* Update simpleaf to 0.19.0

* Update meta.yaml

* Update build.sh

* Update build.sh

* Update build.sh

---------

Co-authored-by: Rob Patro <[email protected]>

* Add osx-arm64 build to py2bit (#53398)

* Build for osx-arm64

* Update meta.yaml

* Update build.sh

* Delete recipes/py2bit/build.sh

* Update meta.yaml

---------

Co-authored-by: Joshua Zhuang <[email protected]>

* Update mummer4 to 4.0.0 (#53477)

* Update mummer4 to 4.0.0

* clean up patches

* add m4

* Update build.sh

---------

Co-authored-by: mencian <[email protected]>
Co-authored-by: Joshua Zhuang <[email protected]>

* Update genomad to 1.9.0 (#53480)

* Fix geNomad 1.9.0 dependencies (#53482)

* Update r-locuszoomr to 0.3.6 (#53483)

* Update doc metadata for eastr (#53481)

* Update grepq to 1.4.3 (#53494)

* Update notramp to 1.1.9 (#53491)

* [biobb_morph] update 5.0.1 (#53492)

* Update r-tidyheatmap to 1.11.4 (#53487)

* Update r-tidyheatmap to 1.11.4

* add run_exports

---------

Co-authored-by: Joshua Zhuang <[email protected]>

* Update perl-io-interactive to 1.026 (#41845)

* Update perl-io-interactive to 1.025

* Update perl-io-interactive to 1.026

* Add run_exports

---------

Co-authored-by: Martin Grigorov <[email protected]>

* Update runjob to 2.10.9 (#49329)

* Update runjob to 2.10.8

* Update meta.yaml

* Update runjob to 2.10.9

* Update meta.yaml

---------

Co-authored-by: Joshua Zhuang <[email protected]>

* miniasm: add arm64 build (#53495)

* unicycler: add aarch64 build (#53496)

* Add recipe for FragGeneScanRs (#53490)

* Add recipe for FragGeneScanRs

* Fix the download url. Add linux-aarch64 and osx-arm64

* Do not run `cargo test` in the test phase.

---------

Co-authored-by: Felix Van der Jeugt <[email protected]>
Co-authored-by: Martin Grigorov <[email protected]>

* Update to v2.7.5 (#53499)

* Manta boost fix: add boost-cpp dependency at runtime. (#53424)

* Add boost-cpp to run dependencies - #53419.

* Bump the build

* Add better error checking for #53419

* Typo.

* Update meta.yaml: make a test that will fail on error

* Update meta.yaml: switch out boost-cpp to libboost in runtime reqs

* Update meta.yaml: remove ':' from test.

* [curves_biobb] update 3.0.3 (#53498)

* [curves_biobb] update 3.0.3

* [curves_biobb] update 3.0.3

* [curves_biobb] update 3.0.3

* [curves_biobb] update 3.0.3

* tgsgapcloser: add aarch64/arm64 builds (#53497)

* tgsgapcloser: add aarch64/arm64 builds

* Update build.sh

* Update build.sh

* Update build.sh

* add patch

* Update build.sh

* add patch

* Update build.sh

* clean up recipe

* clean up recipe

* Update nanomotif to 0.5.5 (#53503)

* Rebuild tgsgapcloser (#53506)

* Rebuild tgsgapcloser

* Update build.sh

* Update Earl Grey meta.yaml (#53507)

* Update meta.yaml

* Update meta.yaml

* Update of ngs-bits to version 2025_01 (#53500)

* Updated ngs-bits to version 2018_10

* bla

* ngs-bits update

* update build

* add haplogrep3 (#53504)

* add haplograph3

* Update nf-core to 3.2.0 (#53509)

* Update earlgrey to 5.1.1 (#53508)

* Update dnachisel to 3.2.13 (#53511)

* Update regenie to 4.1 (#53516)

* Update pangolin-data to 1.32 (#53514)

* Updated eggnog-mapper: Added upper bound on python (#53518)

* Update ms2pip recipe (#53502)

* Update to AMRFinderPlus 4.0.15 (#53515)

* Update pybigwig to 0.3.24 (#53512)

* Update pybwa to 1.4.4 (#53519)

* Update t1k to 1.0.7 (#53521)

* Update gempipe to 1.37.6 (#53523)

* Update snk-cli to 0.7.2 (#53530)

* Update kegg-pathways-completeness to 1.3.0 (#53532)

* Add recipe for GET_PANGENES  (#53489)

* 1st draft

* version 15012025

* remove blank

* 1st draft

* added notes

* removed src_file test and added description

* added HPC instructions

* fails tests

* works with default minimap2, not yet with gsalign

* documented other minimap2 version

* bioconda-utils build --docker --mulled-test --packages get_pangenes ok

* works now with GSAlign

* uses ISO date format for versions and import get_homologues

* Update recipes/get_pangenes/meta.yaml

remove previous minimap2 version

Co-authored-by: Björn Grüning <[email protected]>

* Update recipes/get_pangenes/meta.yaml

removed unused test requirements wget, tar, coreutils (sort)

Co-authored-by: Björn Grüning <[email protected]>

* removed commented out tests

---------

Co-authored-by: eead-csic-compbio <[email protected]>
Co-authored-by: Björn Grüning <[email protected]>

* Update libcifpp to 7.0.9 (#53539)

* [curves_biobb] update 3.0.3b1 (#53524)

* [curves_biobb] update 3.0.3b1

* [curves_biobb] update 3.0.3b1

* [curves_biobb] update 3.0.3b1

* [curves_biobb] update 3.0.3b1

* [curves_biobb] update 3.0.3b1

* [curves_biobb] update 3.0.3b1

* [curves_biobb] update 3.0.3b1

* [curves_biobb] update 3.0.3b1

* Update dependencies (#53531)

* Update excludonfinder to 0.1.3 (#53538)

* Update ucsc-cell-browser to 1.2.10 (#53543)

* Update picrust2 to 2.6.0 (#53510)

* Update picrust2 to 2.6.0

* Update picrust2 to 2.6.0

* Update meta.yaml

* add ete3

---------

Co-authored-by: Joshua Zhuang <[email protected]>

* Update dendropy to 5.0.2 (#53545)

* Update mgnify-pipelines-toolkit to 0.2.1 (#53541)

* Update mgnify-pipelines-toolkit to 0.2.1

* Update meta.yaml

---------

Co-authored-by: Joshua Zhuang <[email protected]>

* Update egglib to 3.3.5 (#53547)

* Update egglib to 3.3.5

* try osx builds

* Update meta.yaml

---------

Co-authored-by: Joshua Zhuang <[email protected]>

* Update pairix to 0.3.9 (#53548)

* Update metabolabpy to 0.9.67 (#53549)

* Update bactopia-py to 1.4.0 (#53551)

* Update bactopia-py to 1.4.0

* add depends

* Update tests

---------

Co-authored-by: Robert A. Petit III <[email protected]>

* Update captus to 1.1.1 (#53546)

* Bump up abnumber to 0.4.3 (#53544)

* Update grepq to 1.4.4 (#53550)

* perl-html-parser: add linux-aarch64, bump build (#53542)

* Update goldrush to 1.2.2 (#53553)

* bioconductor-copynumber restore to enable aarch64 supporting package (#53513)

* Update perl-html-parser to 3.83 (#53554)

* Update vg to v.1.63.1 (#53555)

* Update vvv2_display to 0.2.3.4 (#53557)

* Update pybiolib to 1.2.298 (#53558)

* Update flashlfq to 2.0.0 (#52720)

* Update flashlfq to 2.0.0

* Update meta.yaml

---------

Co-authored-by: Joshua Zhuang <[email protected]>

* maxbin2: start enabling linux-aarch64 (#52771)

* Replace blacklisted perl-lwp-simple with perl-libwww-perl

* spacing for version constraint on perl (don't know if the constraint is necessary)

* maxbin2: Remove perl=5.26 limit - not documented if it is needed and not built on linux-aarch64

* Bump the build number

---------

Co-authored-by: Martin Grigorov <[email protected]>

* Add recipe for pb-CpG-tools (#53520)

* Add recipe for pb-CpG-tools

* Update recipes/pb-cpg-tools/meta.yaml

Co-authored-by: Martin Grigorov <[email protected]>

---------

Co-authored-by: Martin Grigorov <[email protected]>

* Update bioconda-utils to 3.7.1 (#53562)

* Update pacu_snp to 0.0.7 (#53563)

* Update rnanorm to 2.2.0 (#53561)

* hops: update openjdk dependency to enable aarch64 support (#53564)

* perl-lwp-simple: bump the version number of perl-libwww-perl to match (#53560)

* Update rmlst_api to 0.1.6 (#53570)

* Update rmlst_api to 0.1.6

* Update meta.yaml

---------

Co-authored-by: Joshua Zhuang <[email protected]>

* Update harpy to 1.16.2 (#53568)

Co-authored-by: Joshua Zhuang <[email protected]>

* Update superintervals to 0.2.9 (#53559)

* Update superintervals to 0.2.8

* Update superintervals to 0.2.9

* Update meta.yaml

---------

Co-authored-by: Joshua Zhuang <[email protected]>

* Tidy up `vartrix` recipe (#53565)

* no deps; license; bump build; stricter pin

vendoring static binaries

* bundle license

from https://github.com/10XGenomics/vartrix/blob/3dd49885e9c2cdce72b1c0e58e125a5285a184bc/LICENSE

* skip noarch linting

* Update perl-libwww-perl to 6.77 (#53569)

* Update perl-libwww-perl to 6.77

* Update meta.yaml

* Update meta.yaml

* Update meta.yaml

* Update meta.yaml

* Update meta.yaml

---------

Co-authored-by: Joshua Zhuang <[email protected]>

* Update r-ukbrapr to 0.3.0 (#53573)

* Update shasta to 0.14.0 (#53576)

* Update resistify to 1.1.5 (#53575)

* Update snakebids to 0.14.0 (#53578)

* Update jbrowse2 to 3.0.0 (#53577)

* Updated sequenceTools  (#53566)

* updated meta.yaml for sequenceTools

* updated build number

* Update hybracter to 0.11.2 (#53580)

* Update scirpy to 0.20.1 (#53581)

* Update scirpy to 0.20.1

* Fix logomaker dependency

---------

Co-authored-by: Gregor Sturm <[email protected]>

* Update jbrowse2 to 3.0.1 (#53582)

* Update matchtigs to 2.1.9 (#53585)

* Update matchtigs to 2.1.9

Also add a reference to the Eulertigs paper.

* Reset build number to zero.

* Update ms2rescore (#53367)

* Update ms2rescore to 3.1.0

* clean up recipe

* add im2deep

* Update ms2rescore to 3.1.1

* Update ms2rescore to 3.1.2

* Update ms2rescore to 3.1.3

* Update ms2rescore to 3.1.3.post1

* update dependencies

* Update meta.yaml

* Update meta.yaml

* Update ms2rescore to 3.1.4

* Update recipe

* Linter doesn't like tildes

* Relax DeepLC requirement, skip linux-aarch64 build (no tf etc)

* Remove optional pyopenms dependency

* Retry with new pyopenms and ms2pip builds

* Add flit-core dependency

---------

Co-authored-by: BiocondaBot <[email protected]>
Co-authored-by: mencian <[email protected]>
Co-authored-by: Joshua Zhuang <[email protected]>

* Add ESME bundle (Earth System Modelling Environment) - Work in progress (#53556)

* Add ESME bundle

* Enhancements and fixes for ESME bundle:
- Add ParallelIO
- Correct usage of pin_subpackage
- Build for all MPIs
- Add OMB
- Adjust run requirements
- Fix build string
- Skip-lint version_constraints_missing_whitespace
- Add ESMF_CPP

* Build for MPIch only

* Add CPP flags

* Add compilers in run requirements and skip final test for ESME

* Update wipertools to 1.1.5 (#53593)

* Update sylph-tax to 1.1.1 (#53591)

* Update excludonfinder to 0.1.4 (#53590)

* Update harpy to 1.16.3 (#53589)

* Update meta.yaml (#53586)

* Update r-ukbrapr - remove deprecated dependencies (#53592)

* Update snakebids (#53579)

* Update meta.yaml

`raumel_yaml` version >= 0.17.2 doesn't exist on conda-forge

* Bump build number

* change ruamel_yaml to ruamel.yaml

* remove channel pin from ruamel.yaml

* Update dxpy to 0.388.0 (#53598)

* Update augur to 28.0.0 (#53594)

* Update ont-modkit to 0.4.3 (#53597)

* Update nanocaller to 3.6.1 (#53601)

* update dxpy requirements of current recipe to reflect dependencies used for pypi (#53602)

update dxpy requirements to reflect those used for pypi; see:
https://github.com/dnanexus/dx-toolkit/blob/v0.388.0/src/python/requirements.txt
https://github.com/dnanexus/dx-toolkit/blob/master/src/python/setup.py

* Update dxpy: comment out optional extra dependencies (#53603)

* Update dxpy: comment out optional extra dependencies

Update the `dxpy` recipe to comment out optional extra dependencies: pandas, numpy, and xattr since they're somewhat large in size and not required apart from using the `dx extract_dataset` command. A metapackage with these extra dependencies could be added in the future if needed.

* increment build number

* krakenuniq, kmer-jellyfish 1.1.12: enable aarch64, reenable x86 (#53606)

* krakenuniq: add linux-aarch64, bump the build

* kmer-jellyfish 1.1.12: add linux-aarch64 - needed by krakenuniq

* kmer-jellyfish-1.1.12: add linux-aarch64, fix configure error, make -fsigned-char due to (very valid) warnings

* Workaround a broken autoconf setup with jellyfish.
autoconf produces a syntax error in the AS_IF which
I have otherwise been unable to resolve.

* krakenuniq: add build_config

* Update build.sh: add std=c++14 - reqd for os/x compilation

* Update piranha-polio to 1.4.2 (#53604)

* Update piranha-polio to 1.4

* Update piranha-polio to 1.4.1

* Update piranha-polio to 1.4.2

* Update pybwa to 1.4.5 (#53605)

* Update gtotree to 1.8.9 (#53613)

* Update ucsc-cell-browser to 1.2.11 (#53616)

* Update grenedalf to 0.6.3 (#53615)

* Update mutmap to 2.3.9 (#53612)

* Update qtlseq to 2.2.9 (#53610)

* Update nanomotif to 0.5.6 (#53607)

* Update pymzml to 2.5.11 (#53609)

* Update pymzml to 2.5.11

* Update meta.yaml

---------

Co-authored-by: Joshua Zhuang <[email protected]>

* Update genomic_address_service to 0.1.4 (#53618)

* Update `nafcodec` to `v0.3.1` (#53611)

* Update pybwa to 1.4.6 (#53620)

* Enable `linux-aarch64` for `nafcodec` (#53621)

* Update piscem to 0.12.1 (#53622)

* Update grepq to 1.4.5 (#53623)

* Update piscem to 0.12.2 (#53627)

* Update needletail to 0.6.2 (#53628)

* Update needletail to 0.6.2

* Remove `needletail` patch

* Bump minimum `maturin` version

---------

Co-authored-by: Antônio Camargo <[email protected]>

* Update comparem2 to 2.13.1 (#53624)

* Update simpleaf to 0.19.1 (#53631)

* Update simpleaf to 0.19.1

* Update meta.yaml

---------

Co-authored-by: Rob Patro <[email protected]>

* Update msstitch to 3.17 (#53625)

* Update grepq to 1.4.7 (#53632)

* Update twopaco to 1.1.0 (#53630)

* Update twopaco to 1.1.0

* Update meta.yaml

---------

Co-authored-by: Joshua Zhuang <[email protected]>

* Update NanoPlot to v1.44.1 (#53635)

* Update NanoPlot to v1.44.1

for some reason, need capitalized NanoPlot again in the URL. Not sure

* woopsie

* reset build number

* Add `osx-arm64` build to `pydustmasker` (#53629)

* Add `osx-arm64` build to `pydustmasker`

* Skip `version_constraints_missing_whitespace` lint

* Update truvari to 5.1.0 (#53636)

* Update dfast to 1.3.5 (#53637)

* Add EGAP recipe (#53614)

* Add EGAP recipe

* Update EGAP meta.yaml and build.sh for stable tarball and sha256

* Fix lint errors: matplotlib-base, run_exports, compilers in build

* Fix lint build errors to Update EGAP recipe

* Update meta.yaml reduced python version limit to <3.9

* Update meta.yaml removed  script: bash build.sh

* Update meta.yaml set compiler from 'cxx' -> 'c'

* Update meta.yaml updated compiler to have BOTH 'c' and 'cxx'

* Update build.sh added make CC="$CC"

* Update meta.yaml added zlib to host and run

* Update meta.yaml updated to have zlib >=1.2.13,<1.30

* Update meta.yaml updated quast to 5.3.0 and zlib set to 1.3

* Update meta.yaml updated zlib and python build allowances

* Update build.sh added exports for CPPFLAGS and LDFLAGS

We export CPPFLAGS and LDFLAGS to ensure we can find zlib.h and libz.so.
In the make command for purge_dups, we explicitly pass CC="$CC" and LDFLAGS="$LDFLAGS" to avoid “cannot find -lz.”
If purge_dups’s Makefile tries to do something like gcc calcuts.o -lz, it will see -L$PREFIX/lib from $LDFLAGS and properly locate libz.

* Delete recipes/egap/build.sh

Ratatosk and purge_dups can be installed via conda

* Update meta.yaml removed build.sh requirements moved into conda installs

ratatosk =0.9.0
purge_dups =1.2.6

Removed depencies found in the build.sh (and the file itself) now that that they can be called via python.

* Update meta.yaml to guarantee that there should be linux specific

Made exclusive linux distribution

* Update meta.yaml attempting to set as noarch

* Update meta.yaml attempted to update to noarch

* Update meta.yaml corrected adding EGAP.py to bin

* Update meta.yaml with shebang

* Update meta.yaml updated with shebang fixes

* Update meta.yaml added run_exports and corrected dependencies

* Update meta.yaml to resolve reviewer comments

Adjusted the tarbal url to use "version" instead of hardcoded number.

Moved python and co to host.

Use >= instead of = to loosen version restrictions.

* Update meta.yaml updated flye version, removed zlib and java requirements

* Update meta.yaml updated to v2.5.3

Updated to new tarball

* Add a3partitioner v0.1.0 (#53633)

* Add a3partitioner v0.1.0

* Add run_exports to a3partitioner recipe

* .

* Update meta.yaml following working example

* Update a3partitioner recipe with working build configuration

* Apply suggestions from code review

---------

Co-authored-by: Martin Grigorov <[email protected]>

* Update pathogen-profiler to 4.7.0 (#53643)

* Update perl-perl-version to 1.018 (#45060)

* Update perl-perl-version to 1.015

* Update perl-perl-version to 1.016

* Update perl-perl-version to 1.017

* Update perl-perl-version to 1.018

* Add run_exports

---------

Co-authored-by: Martin Grigorov <[email protected]>

* SPP-DCJ (#53626)

* Update gfaffix to 0.1.2.2

* Update gfaffix to 0.2.0

* Use compiler(rust)

* add macos-arm64/linux-aarch64 support; improve build.sh

* initial commit

* Update meta.yaml

matplotlib -> matpliblib-base

* Update meta.yaml

Remove unnecessary lines in test

---------

Co-authored-by: BiocondaBot <[email protected]>
Co-authored-by: Martin Grigorov <[email protected]>
Co-authored-by: Dany Doerr <[email protected]>

* Update pybiolib to 1.2.347 (#53641)

* Update parascopy to 1.17.4 (#53645)

* Update deeplc to 3.1.5 (#53653)

* Update vsearch to 2.29.3 (#53654)

* Update deeplcretrainer to 1.0.2 (#53660)

* twopaco: add aarch64/arm64 builds (#53638)

* twopaco: add aarch64/arm64 builds

Signed-off-by: Martin Tzvetanov Grigorov <[email protected]>

* Fix the path to the built binaries

Signed-off-by: Martin Tzvetanov Grigorov <[email protected]>

---------

Signed-off-by: Martin Tzvetanov Grigorov <[email protected]>

* perl-gd & perl-gdtextutil: add aarch64/arm64 builds (#53608)

* fastx_toolkit: add aarch64/arm64 builds

Signed-off-by: Martin Tzvetanov Grigorov <[email protected]>

* perl-gd: add aarch64/arm64 builds

Signed-off-by: Martin Tzvetanov Grigorov <[email protected]>

* Add `expat` as a host dependency for perl-gd

```
 the PKG_CONFIG_PATH environment variable␛[0m
12:56:51 ␛[32mBIOCONDA INFO␛[0m (OUT) Package 'expat', required by 'fontconfig', not found␛[0m
```

Signed-off-by: Martin Tzvetanov Grigorov <[email protected]>

* perl-gdtextutil: add aarch64/arm64 builds

Signed-off-by: Martin Tzvetanov Grigorov <[email protected]>

* Update perl-gd to 2.83

Signed-off-by: Martin Tzvetanov Grigorov <[email protected]>

* Add perl-file-which as a host requirement for perl-gd

Signed-off-by: Martin Tzvetanov Grigorov <[email protected]>

* Add perl-test-nowarnings as a host dependency to perl-gd

Signed-off-by: Martin Tzvetanov Grigorov <[email protected]>

* Do not import modules which $VERSION is not 2.83

Signed-off-by: Martin Tzvetanov Grigorov <[email protected]>

* Disable aarch64/arm64 for now

Signed-off-by: Martin Tzvetanov Grigorov <[email protected]>

* Do not build for osx-arm64. perl-extutils-constant is not available

Signed-off-by: Martin Tzvetanov Grigorov <[email protected]>

* Run `make test` only for Linux

OSX-64 fails with:
```
21:56:54 BIOCONDA INFO (OUT) t/GD.t ....................
21:56:54 BIOCONDA INFO (OUT) Dubious, test returned 255 (wstat 65280, 0xff00)
21:56:54 BIOCONDA INFO (OUT) Failed 13/15 subtests
``

Signed-off-by: Martin Tzvetanov Grigorov <[email protected]>

* Revert fastx_toolkit changes

Signed-off-by: Martin Tzvetanov Grigorov <[email protected]>

---------

Signed-off-by: Martin Tzvetanov Grigorov <[email protected]>

* Update gtotree to 1.8.10 (#53666)

* Update ntm-profiler to 0.6.0 (#53646)

* Update ntm-profiler to 0.6.0

* update recipe deps

---------

Co-authored-by: Jody Phelan <[email protected]>

* Update deeplc to 3.1.7 (#53661)

Co-authored-by: Joshua Zhuang <[email protected]>

* Update eukcc to 2.1.3 (#53659)

* Update eukcc to 2.1.3

* add run_exports

* Update meta.yaml

---------

Co-authored-by: Joshua Zhuang <[email protected]>

* Update HATCHet to v2.1.1 (#53664)

* Egap recipe update (#53662)

* Update meta.yaml (#53668)

* Update meta.yaml (#53663)

* Update sylph-tax recipe (fix python versioning) (#53658)

* Update GW to v1.1.3 (#53670)

* Update taxopy to 0.14.0 (#53672)

* Update taxopy to 0.14.0

* Update `run_exports`

* Update install script

---------

Co-authored-by: Antônio Camargo <[email protected]>

* Update rdeval to 0.0.5 (#53619)

* Update rdeval to 0.0.5

* edit patches

---------

Co-authored-by: mencian <[email protected]>

* Rebuild hatchet (#53673)

* Add recipe for ctyper v1.0 (#53674)

* Add recipe for ctyper v1.0

* Update build.sh

* Update build.sh

* Fix the license file name

---------

Co-authored-by: Martin Grigorov <[email protected]>

* Update dfast_qc to 1.0.6 (#53677)

* UPDATE troubleshoot transannot build (#53488)

* troubleshoot

* troubleshoot

* troubleshoot

* troubleshoot

* Update meta.yaml

* Update meta.yaml after the review

* Update excludonfinder to 0.1.4 (#53596)

* Update excludonfinder to 0.1.4

* Update excludonfinder: increment build number and add run_exports

---------

Co-authored-by: Alvarosmb <[email protected]>

* fastx_toolkit: add linux-aarch64 build (#53667)

* fastx_toolkit: add linux-aarch64 build

Signed-off-by: Martin Tzvetanov Grigorov <[email protected]>

* Use newer config.sub/.guess for aarch64 support

Signed-off-by: Martin Tzvetanov Grigorov <[email protected]>

* Update build.sh

* Update meta.yaml

* Update build.sh

* Update build.sh

* Update build.sh

* Update build.sh

* Update meta.yaml

* Update build.sh

* Update meta.yaml

* Update fastx.patch

* add patch

* Update meta.yaml

* add macos patch

* Update build.sh

* Update build.sh

---------

Signed-off-by: Martin Tzvetanov Grigorov <[email protected]>
Co-authored-by: Joshua Zhuang <[email protected]>
Co-authored-by: mencian <[email protected]>

* Update ESME for CESM compatibility, relax version constraints, and fix licensing: (#53642)

- Relax version requirements for compilers and MPI.
- Added copyrights for NetCDF
- Changed license type for PnetCDF and ESMF

* Update vvv2_display to 0.2.3.5 (#53678)

* Update seismic-rna to 0.23.0 (#53675)

* Update seismic-rna to 0.23.0

* Update meta.yaml

* Update build.sh

* Delete recipes/seismic-rna/build.sh

* Update meta.yaml

---------

Co-authored-by: Joshua Zhuang <[email protected]>

* Add magneto (#53583)

* add magneto recipe

* Update meta.yaml

---------

Co-authored-by: Joshua Zhuang <[email protected]>

* update transannot after the 2nd revision (#53452)

* update transannot after the 2nd revision

* Update meta.yaml

* Update build.sh

* Update meta.yaml

* Update build.sh

* Update build.sh

* Update build_failure.osx-arm64.yaml

* Delete recipes/transannot/build_failure.osx-arm64.yaml

* Update build.sh

---------

Co-authored-by: Joshua Zhuang <[email protected]>

* Update cramino to 0.16.0 (#53679)

* Update cramino to 0.16.0

* change build to 0

---------

Co-authored-by: Alexandra Pancikova <[email protected]>

* Update seqnado to 0.6.0 (#53682)

* Update mummer4 to 4.0.1 (#53683)

* Mash patch fixes: resolve build failures on Linux (#53680)

* mash: add linux-aarch64 build

Signed-off-by: Martin Tzvetanov Grigorov <[email protected]>

* Try with `libzlib` instead of `zlib`

Trying to solve:
```
Encountered problems while solving:
12:56:27 BIOCONDA INFO (OUT)   - package capnproto-1.0.2-h8ea4ab2_2 requires libzlib >=1.3.1,<2.0a0, but none of the providers can be installed
12:56:27 BIOCONDA INFO (OUT) 
12:56:27 BIOCONDA INFO (OUT) Could not solve for environment specs
12:56:27 BIOCONDA INFO (OUT) The following packages are incompatible
12:56:27 BIOCONDA INFO (OUT) ├─ capnproto 1.0.2.*  is installable and it requires
12:56:27 BIOCONDA INFO (OUT) │  └─ libzlib >=1.3.1,<2.0a0  with the potential options
12:56:27 BIOCONDA INFO (OUT) │     ├─ libzlib 1.3.1 would require
12:56:27 BIOCONDA INFO (OUT) │     │  └─ zlib 1.3.1 *_0, which can be installed;
12:56:27 BIOCONDA INFO (OUT) │     ├─ libzlib 1.3.1 would require
12:56:27 BIOCONDA INFO (OUT) │     │  └─ zlib 1.3.1 *_1, which can be installed;
12:56:27 BIOCONDA INFO (OUT) │     └─ libzlib 1.3.1 would require
12:56:27 BIOCONDA INFO (OUT) │        └─ zlib 1.3.1 *_2, which can be installed;
12:56:27 BIOCONDA INFO (OUT) └─ zlib 1.2.*  is not installable because it conflicts with any installable versions previously reported
```

* Re-add zlib as dependency

* Try with zlib 1.3.*

* Update meta.yaml

* Update build.sh

* bump build number

* Update build.sh

* add limits patch to relax compiler version

* Fix C++ compiler version to handle uint32_t without include

* mash:
don't wrap memcpy: only needed for distributing to support older Linux versions.
bioconda shouldn't need this.  marbl/Mash#103

* add patch

* Update meta.yaml: remove osx-arm64

Is already a skip for OS/X x86.  Should resolve separately to this.

* Update meta.yaml: restore osx-arm64

* Add std=c++14 to compile with capnproto on os/x

* Update conda_build_config.yaml: use later os/x compiler

* don't link non-existent librt on Darwin

---------

Signed-off-by: Martin Tzvetanov Grigorov <[email protected]>
Co-authored-by: Martin Tzvetanov Grigorov <[email protected]>
Co-authored-by: Andreas Sjödin <[email protected]>
Co-authored-by: Martin Grigorov <[email protected]>
Co-authored-by: Joshua Zhuang <[email protected]>

* Update manta - Add back missing scripts (#53640)

* update yaml (#53681)

* krbalancing: add arm64 build (#53688)

* update biobox_add_tagid (#53685)

* Update gseapy to 1.1.5 (#53696)

* Update oakvar to 2.12.9 (#53693)

* Updating bioconductor-limma for osx-arm64 (#53690)

* Updating bioconductor-pcamethods for osx-arm64 (#53694)

* Updating bioconductor-biocparallel for osx-arm64 (#53697)

* Update meta.yaml for NanoCaller (#53698)

* Update panacus recipe to include third-party licenses (#53676)

* Bump panacus version

* Add cargo bundle licenses

* Reset build number

* Update panacus to include serde derive feature

* Add THIRDPARTY.yml to licence_file

* s/-/./ in version

* Bump panacus version

* Update build.sh

---------

Co-authored-by: Peter Heringer <[email protected]>
Co-authored-by: Martin Grigorov <[email protected]>
Co-authored-by: Joshua Zhuang <[email protected]>

* Update tmalign to 20190818 (#53699)

* Update tmalign to 20190818

* Update meta.yaml

* Update r-jackstraw to 1.3.17 (#53119)

* Update r-jackstraw to 1.3.17

* Update meta.yaml

* Update build.sh

---------

Co-authored-by: Joshua Zhuang <[email protected]>

* Update perl-data-uuid to 1.227 (#53117)

* Update perl-data-uuid to 1.227

* Update meta.yaml

---------

Co-authored-by: Joshua Zhuang <[email protected]>

* dialign-tx: add arm64 build (#53700)

* Update perl-datetime to 1.65 (#53132)

* Update perl-datetime to 1.65

* add run_exports

---------

Co-authored-by: Joshua Zhuang <[email protected]>

* perl-data-uuid: add aarch64/arm64 builds (#53701)

* perl-data-uuid: add aarch64/arm64 builds

Signed-off-by: Martin Tzvetanov Grigorov <[email protected]>

* Do not build osx-arm64. It depends on missing dependencies

---------

Signed-off-by: Martin Tzvetanov Grigorov <[email protected]>

* Update perl-cgi to 4.67 (#53120)

* Update perl-cgi to 4.66

* Update perl-cgi to 4.67

* Update meta.yaml

* Update meta.yaml

* Disable the test for CGI::Cookie. It's version is 4.59 instead of 4.67

Signed-off-by: Martin Tzvetanov Grigorov <[email protected]>

* Add builds for aarch64 and arm64

Signed-off-by: Martin Tzvetanov Grigorov <[email protected]>

* Do not build aarch64 and arm64. perl-sub-uplevel is not yet available for them

---------

Signed-off-by: Martin Tzvetanov Grigorov <[email protected]>
Co-authored-by: Joshua Zhuang <[email protected]>
Co-authored-by: Martin Tzvetanov Grigorov <[email protected]>
Co-authored-by: Martin Grigorov <[email protected]>

* Update perl-template-toolkit to 3.102 (#53112)

* Update perl-template-toolkit to 3.102

* add run_exports

* Add run_exports

Signed-off-by: Martin Tzvetanov Grigorov <[email protected]>

* Update the expected version in the tests

Signed-off-by: Martin Tzvetanov Grigorov <[email protected]>

* Try to build for aarch64 and arm64

---------

Signed-off-by: Martin Tzvetanov Grigorov <[email protected]>
Co-authored-by: Joshua Zhuang <[email protected]>
Co-authored-by: Martin Tzvetanov Grigorov <[email protected]>
Co-authored-by: Martin Grigorov <[email protected]>

* clustalw: add arm64 build (#53702)

* Add muset recipe (#53080)

* Add kmtricks dependency to decom recipe

* increment build number and remove noarch specification

* Increment build number

* Add noarch: python and setuptools

* Resolve conflicts in decom recipe

* Add muset recipe version 0.5.1

* Add muset recipe version 0.5.1

- Add run_exports to build section
- Follows Bioconda linting guidelines

* Add muset recipe v0.5.1

- Added run_exports for dependency pinning
- Specified build script location
- Added pkg-config and libstdcxx-ng to dependencies

* Remove build.sh script

* Minimal muset recipe

* Add run_exports to build section

* Simplify build.sh script

* Improve muset recipe build configuration

- Add make and pkg-config to build requirements
- Update build script to explicitly set compiler paths

* Add recursive flag to git clone

* Add git recursive to build.sh

* add git dependency to meta.yaml!

* Simplify muset recipe build process

* Update muset recipe to explicitly set CONDA_BUILD=ON for proper conda packaging

* Add patch for fmt external project in muset

* add external projects patch

* Try original conda recipe

* run exports + reset build number + summary

* Add verbose build.sh

* Try external projects patch

* Modify ExternalProject configurations to prevent library downloads and improve Bioconda build compatibility for bundled external libraries.

* Fix xxHash library patch for Bioconda build

* go back to simpler external_proj_projects.patch

* go back to simpler patch

* add one path per external project

* fix indentation error in meta.yaml

* Edit white spaces and indentation in patches

* Ensure newline at the end of every patchç

* Try verbose build to debug patches

* Going back to standard build + no patches

* correct build.sh that points to non existing patch

* Try only fmt patch

* remove trash file

* added verbose build + modified fmt patch

* Add an even more verbose build.sh

* Attempt to fmt patch

* Avoid unnecessary download in fmt patch

* adapt build.sh

* Correct fmt patch

* No patches

* Explicitly set some variables in build.sh

* add cmake path to build.sh

* add alternative fmt patch

* Try adding dependencies from conda directly

* remove duplicated compiler

* Remove compiler from host section in meta.yaml

* Navigate muset as subdirectory in build.sh

* Remove external ref to build.sh in meta.yaml

* Change build.sh to verify folder structure is correct

* list external directories

* specify git version and recursive git cloning

* try git commands inside build.sh

* git checkout from the version which is passed as an env variable

* git init before git fetch

* Fix version for checkout using version tag

* remove any existing directories to prevent issues

* Undo the rm -rf .git action and simply git submodule init and update recursively

* Verbose build.sh to find executables

* fix build.sh to avoid copying non-existing binaries

* add check for dynamic dependencias in bin folder and add test commands in meta.yaml

* Change print binary informaiton after copying files, remove use of command file

* Remove test section

* actually tests can't be removed :)

* Remove git init and remote add origin commands from build.sh

* Try different url

* add additional echo test after muset --help

* Explicitly exit with success statusç

* More verbose build.sh to see if binary copying suceeds

* Add verbose version of build.sh

* add more verbose build.sh

* Added a run_test.sh file

* Uset git_url in meta.yaml and remove git init in build.sh

* Add sha256

* Remove checksum

* Extra note to skip lint as no checksum will be provided

* Add skip-lints missing hash

* Keep old run_test.sh file

* Minor cleanup of build.sh

* Remove default values to simplify the config

* Update meta.yaml

* cmake --verbose

* Do not build for linux-aarch64. It uses x86_64 intrinsics and needs patching for ARM NEON

* fix run_test.sh to remove || echo and || true fallbacks

* Try simpler  run_test.sh script

* Edit run_test.sh since exit was in the middle of the file

* remove ldd command

* Try simpler run_test.sh script

* More verbose run_test.sh

* Check muset --help output

* Add test commands on meta.yaml only

* It looks like `--version` returns non-0 status code. Pipe it to grep to recover

* '--help' returns non-0 status code. Pipe it to `grep` to recover

---------

Co-authored-by: Martin Grigorov <[email protected]>

* Update perl-file-copy-link to 0.200 (#53109)

* Update perl-file-copy-link to 0.200

* Update meta.yaml

* Update version.patch

* No need to patch the version

* Delete recipes/perl-file-copy-link/version.patch

* Try to build for aarch64 and arm64

* Do not build osx-arm64. perl-data-dumper is not yet available

---------

Co-authored-by: Joshua Zhuang <[email protected]>
Co-authored-by: Martin Grigorov <[email protected]>

* Update trackplot to 0.5.2 (#53704)

* perl-params-validate: add linux-aarch64 (#53705)

* Add linux-aarch64

* declare name

* add Vpt segmentation packing (#53649)

* add vpt-segmentation-packing

* update meta

* Update recipes/vpt-segmentation-packing/meta.yaml

Co-authored-by: Björn Grüning <[email protected]>

* pin python version

---------

Co-authored-by: Björn Grüning <[email protected]>

* Update pysam to 0.23.0 (#53706)

* create corona_lineage_dynamics (#53522)

* create corona_lineage_dynamics

* Update recipes/corona_lineage_dynamics/build.sh

Co-authored-by: Martin Grigorov <[email protected]>

* Update recipes/corona_lineage_dynamics/meta.yaml

Co-authored-by: Martin Grigorov <[email protected]>

* fixing errors by bio-conda

* fixing errors

* Fixed issues as per review comments

* Fixed issues as per review comments

* library link changed

* Fixed issues as per review comments

* Fixed issues as per review comments

* Fixed issues as per review comments

* Fixed issues as per review comments

* Fixed issues as per review comments

* Cleanup meta.yaml

* Update meta.yaml

* Remove the version range for r-base

For some reason conda-build does not like it:
```
conda.exceptions.InvalidVersionSpec: Invalid version '>=4': invalid character(s)
```

* Do not build aarch64 and arm64. r-binom is not yet available for them

---------

Co-authored-by: Martin Grigorov <[email protected]>

* Update recipe for corona_lineage_dynamics: r-xml is added as a requir… (#53710)

* Update recipe for corona_lineage_dynamics: r-xml is added as a required package.

* Update recipe for corona_lineage_dynamics: r-xml is added as a required package.

* Update truvari to 5.1.1 (#53711)

* Update tower-cli to 0.11.0 (#53712)

* Update biobox_add_taxid to 1.1 (#53713)

* Update dendropy to 5.0.3 (#53714)

* Update dendropy to 5.0.4 (#53717)

* Update taseq to 1.1.1 (#53720)

* Update dendropy to 5.0.5 (#53721)

* Updating bioconductor-globalancova for osx-arm64 (#53718)

* Updating bioconductor-globalancova for osx-arm64

* Updating bioconductor-graph for osx-arm64

* Updating bioconductor packages for osx-arm64 (#53715)

* Update biox to 1.2.0 (#53716)

* Update biox to 1.2.0: fix taxonomy dependency

* Update biox to 1.2.0

* Update biox to 1.2.0

* Update biox to 1.2.0

* Update biox to 1.2.0

* Update dendropy to 5.0.6 (#53722)

Co-authored-by: Martin Grigorov <[email protected]>

* Update pybiolib to 1.2.366 (#53724)

* Update learnmsa to 2.0.10 (#53725)

* Updating bioconductor packages for osx-arm64 (#53719)

* Update amplify to 2.0.1 (#53728)

* Update seqnado to 0.6.1 (#53729)

* Update ncbi-stxtyper to 1.0.40 (#53734)

* Updating bioconductor-rbgl for osx-arm64 (#53736)

* Updating bioconductor-multtest for osx-arm64 (#53735)

* Updating bioconductor-msnbase for osx-arm64 (#53733)

* Add linux-aarch64 to bioconductor-globalancova (#53723)

Signed-off-by: Martin Tzvetanov Grigorov <[email protected]>

* Update biobox_add_taxid to 1.2 (#53741)

* Update freyja to 1.5.3 (#53740)

* Update for AMRFinderPlus 4.0.19 (#53738)

* Updating bioconductor-camera for osx-arm64 (#53739)

* Updating bioconductor-fgsea version, osx-arm64 (#53737)

* Add adas v0.1.2 (#53742)

* Add adas v0.1.2

* Add adas v0.1.2

* Collect third party licenses with cargo-bundle-licenses. Add linux-aarch64

* collect third party licences

* Drop linux-aarch64. A dependency does not compile on this platform

---------

Co-authored-by: Jianshu Zhao <[email protected]>
Co-authored-by: Martin Grigorov <[email protected]>

* Update seqnado dependencies (#53731)

* Update seqnado dependencies: replace click, cookiecutter, and drmaa with pandera and pyranges; update pulp version and refine snakemake constraints.

* Refine formatting of dependency constraints in seqnado meta.yaml

* Bump build number to 1 in seqnado meta.yaml

* Update perl-mime-types to 2.27 (#45653)

* Update perl-mime-types to 2.26

* Update perl-mime-types to 2.27

* Add run_exports

---------

Co-authored-by: Martin Grigorov <[email protected]>

* Relax run requirements (#53743)

* Relax run requirements for compilers & MPI

* Bump build number

* Change syntax

* Start with MPI for run requirements

* Fix indentation

* Use a single line for {% if mpi_name == ...

* Update meta.yaml (#53745)

* Update gw to 1.1.4 (#53746)

* genoflu version 1.06

---------

Signed-off-by: Martin Tzvetanov Grigorov <[email protected]>
Co-authored-by: Bioconda Bot <[email protected]>
Co-authored-by: Florian Zwagemaker <[email protected]>
Co-authored-by: Timo Sachsenberg <[email protected]>
Co-authored-by: Martin Grigorov <[email protected]>
Co-authored-by: James A. Fellows Yates <[email protected]>
Co-authored-by: Rob Patro <[email protected]>
Co-authored-by: Filipe G. Vieira <[email protected]>
Co-authored-by: Konstantinn Bonnet <[email protected]>
Co-authored-by: Harrison Deng <[email protected]>
Co-authored-by: Rutger Vos <[email protected]>
Co-authored-by: Joshua Zhuang <[email protected]>
Co-authored-by: Wolfgang Maier <[email protected]>
Co-authored-by: mencian <[email protected]>
Co-authored-by: Antônio Camargo <[email protected]>
Co-authored-by: coperni <[email protected]>
Co-authored-by: Pau Andrio <[email protected]>
Co-authored-by: Felix Van der Jeugt <[email protected]>
Co-authored-by: Felix Van der Jeugt <[email protected]>
Co-authored-by: nickjcroucher <[email protected]>
Co-authored-by: dslarm <[email protected]>
Co-authored-by: Genís Bayarri <[email protected]>
Co-authored-by: Tobias Baril <[email protected]>
Co-authored-by: Marc Sturm <[email protected]>
Co-authored-by: Ramprasad Neethiraj <[email protected]>
Co-authored-by: Usman Rashid <[email protected]>
Co-authored-by: Ralf Gabriels <[email protected]>
Co-authored-by: Arjun Prasad <[email protected]>
Co-authored-by: Michael S. Cuoco <[email protected]>
Co-authored-by: brunocontrerasmoreira <[email protected]>
Co-authored-by: eead-csic-compbio <[email protected]>
Co-authored-by: Björn Grüning <[email protected]>
Co-authored-by: Robert A. Petit III <[email protected]>
Co-authored-by: David Příhoda <[email protected]>
Co-authored-by: Felix Mölder <[email protected]>
Co-authored-by: Chris Saunders <[email protected]>
Co-authored-by: Mervin Fansler <[email protected]>
Co-authored-by: Stephan Schiffels <[email protected]>
Co-authored-by: Gregor Sturm <[email protected]>
Co-authored-by: Sebastian Schmidt <[email protected]>
Co-authored-by: Jean Iaquinta <[email protected]>
Co-authored-by: nsandau <[email protected]>
Co-authored-by: Dhananjhay Bansal (Djay) <[email protected]>
Co-authored-by: Chris Tomkins-Tinch <[email protected]>
Co-authored-by: Martin Larralde <[email protected]>
Co-authored-by: Wouter De Coster <[email protected]>
Co-authored-by: Ian M. B. <[email protected]>
Co-authored-by: DaanJansen94 <[email protected]>
Co-authored-by: Daniel Doerr <[email protected]>
Co-authored-by: Dany Doerr <[email protected]>
Co-authored-by: Jody Phelan <[email protected]>
Co-authored-by: RunpengLuo <[email protected]>
Co-authored-by: Steven Sutcliffe <[email protected]>
Co-authored-by: Jim Shaw <[email protected]>
Co-authored-by: Kez Cleal <[email protected]>
Co-authored-by: Mariia Zelenskaia <[email protected]>
Co-authored-by: Alvarosmb <[email protected]>
Co-authored-by: Alvarosmb <[email protected]>
Co-authored-by: Hugo Lefeuvre <[email protected]>
Co-authored-by: Alexandra P <[email protected]>
Co-authored-by: Alexandra Pancikova <[email protected]>
Co-authored-by: Martin Tzvetanov Grigorov <[email protected]>
Co-authored-by: Andreas Sjödin <[email protected]>
Co-authored-by: Pontus Höjer <[email protected]>
Co-authored-by: SantaMcCloud <[email protected]>
Co-authored-by: Tyler Funnell <[email protected]>
Co-authored-by: Sebastian Bassi <[email protected]>
Co-authored-by: Peter Heringer <[email protected]>
Co-authored-by: Peter Heringer <[email protected]>
Co-authored-by: Camila Duitama <[email protected]>
Co-authored-by: Amirhossein <[email protected]>
Co-authored-by: Hadi <[email protected]>
Co-authored-by: TianMayCry9 <[email protected]>
Co-authored-by: Felix Becker <[email protected]>
Co-authored-by: Jianshu_Zhao <[email protected]>
Co-authored-by: Jianshu Zhao <[email protected]>
Co-authored-by: Alastair Smith <[email protected]>