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Merge pull request #61 from databio/dev
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Release 0.8
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jpsmith5 authored Sep 18, 2018
2 parents 6b9f644 + 791095f commit 28263b3
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16 changes: 16 additions & 0 deletions CHANGELOG.md
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# Change log
All notable changes to this project will be documented in this file.

## [0.8.0] -- 2018-09-18

### Added
- Report NRF, PBC1, and PBC2
- Produce bigBed formatted narrowPeak file
- Add plotting of fractions of reads in *any* annotated feature
- Add peak annotation plotting
- Add buffered fastq repair tool

### Changed
- Fixed a bug with alignment rate reporting to prealignments
- Speed up prealignments by leveraging SE alignment
- Fix plotting of unaligned reads
- Fix SE incompatibility
- Rename output files for improved readability

## [0.7.0] -- 2018-06-25

### Added
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18 changes: 11 additions & 7 deletions containers/pepatac.Dockerfile
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Expand Up @@ -5,7 +5,7 @@ FROM phusion/baseimage:0.10.1
LABEL maintainer Jason Smith "[email protected]"

# Version info
LABEL version 0.8.1
LABEL version 0.8.2

# Use baseimage-docker's init system.
CMD ["/sbin/my_init"]
Expand Down Expand Up @@ -45,16 +45,20 @@ RUN pip install virtualenv && \

# Install R
RUN DEBIAN_FRONTEND=noninteractive apt-get --assume-yes install r-base r-base-dev && \
echo "r <- getOption('repos'); r['CRAN'] <- 'http://cran.us.r-project.org'; options(repos = r);" > ~/.Rprofile && \
Rscript -e "install.packages('devtools')" && \
Rscript -e "devtools::install_github('pepkit/pepr')" && \
Rscript -e "install.packages('gtable')" && \
echo "r <- getOption('repos'); r['CRAN'] <- 'http://cran.us.r-project.org'; options(repos = r);" > ~/.Rprofile && \
Rscript -e "install.packages('argparser')" && \
Rscript -e "install.packages('devtools')" && \
Rscript -e "devtools::install_github('pepkit/pepr')" && \
Rscript -e "install.packages('data.table')" && \
Rscript -e "source('https://bioconductor.org/biocLite.R')" && \
Rscript -e "source('https://bioconductor.org/biocLite.R'); biocLite('GenomicRanges')" && \
Rscript -e "devtools::install_github('databio/GenomicDistributions')" && \
Rscript -e "install.packages('ggrepel')" && \
Rscript -e "install.packages('ggplot2')" && \
Rscript -e "install.packages('gplots')" && \
Rscript -e "install.packages('grid')" && \
Rscript -e "install.packages('grid')" && \
Rscript -e "install.packages('gtable')" && \
Rscript -e "install.packages('scales')" && \
Rscript -e "install.packages('data.table')" && \
Rscript -e "install.packages('stringr')"


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4 changes: 2 additions & 2 deletions examples/test_project/test_config.yaml
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Expand Up @@ -18,8 +18,8 @@ data_sources: # This section describes paths to your data
# Variable syntax: {column_name}. For example, use {sample_name} to populate
# the file name with the value in the sample_name column for each sample.
# example_data_source: "/path/to/data/{sample_name}_R1.fastq.gz"
test_data_R1: "$CODEBASE/pepatac/examples/test_data/{sample_name}_r1.fastq.gz"
test_data_R2: "$CODEBASE/pepatac/examples/test_data/{sample_name}_r2.fastq.gz"
test_data_R1: "$CODEBASE/pepatac/examples/data/{sample_name}_r1.fastq.gz"
test_data_R2: "$CODEBASE/pepatac/examples/data/{sample_name}_r2.fastq.gz"

implied_columns:
organism:
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2 changes: 2 additions & 0 deletions examples/tutorial/tutorial.csv
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sample_name,protocol,organism,read1,read2,read_type
tutorial,ATAC,human,tutorial_r1,tutorial_r2,paired
19 changes: 19 additions & 0 deletions examples/tutorial/tutorial.yaml
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name: tutorial

metadata:
sample_annotation: tutorial.csv
output_dir: "$PROCESSED/tutorial/"
pipeline_interfaces: "$CODEBASE/pepatac/pipeline_interface.yaml"

derived_columns: [read1, read2]

data_sources:
tutorial_r1: "$CODEBASE/pepatac/examples/data/tutorial_r1.fastq.gz"
tutorial_r2: "$CODEBASE/pepatac/examples/data/tutorial_r2.fastq.gz"

implied_columns:
organism:
human:
genome: hg38
macs_genome_size: hs
prealignments: rCRSd human_repeats
34 changes: 7 additions & 27 deletions pipeline_interface.yaml
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Expand Up @@ -17,9 +17,14 @@ pipelines:
"--single-or-paired": read_type
optional_arguments:
"--input2": read2
"--peak-caller": peak_caller
"--frip-ref-peaks": FRIP_ref
"--prealignments": prealignments
"--genome-size": macs_genome_size
"--anno-name": anno_name
"--TSS-name": TSS_name
"--keep": keep
"--noFIFO": no_fifo
compute:
singularity_image: ${SIMAGES}pepatac
docker_image: databio/pepatac
Expand All @@ -44,33 +49,8 @@ pipelines:
resources:
default:
file_size: "0"
cores: "2"
mem: "4000"
time: "0-04:00:00"
femto:
file_size: "0.001"
cores: "1"
mem: "4000"
time: "00:40:00"
pico:
file_size: "0.05"
cores: "1"
mem: "4000"
time: "02:00:00"
nano:
file_size: "0.5"
cores: "4"
mem: "16000"
time: "00-04:00:00"
micro:
file_size: "1"
cores: "8"
mem: "32000"
time: "02-00:00:00"
milli:
file_size: "10"
cores: "16"
mem: "64000"
time: "03-00:00:00"
mem: "16000"
time: "0-04:00:00"


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