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‎CHANGELOG.md‎

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# Change log
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All notable changes to this project will be documented in this file.
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## [0.7.0] -- Unreleased
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## [0.7.0] -- 2018-06-25
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### Added
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- Added containerization feature
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- Run with either [docker](https://www.docker.com/) or [singularity](https://singularity.lbl.gov/)
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- Added early bowtie2 index check
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### Changed
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- Renamed pipeline
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- Improved summary figure reporting
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- Integrated summary results into pipeline interface
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## [0.6.1] -- 2017-12-15
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‎Makefile‎

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microtest:
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python $$CODEBASE/ATACseq/pipelines/ATACseq.py -I $$MICROTEST/data/atacR1.fq.gz -I2 $$MICROTEST/data/atacR2.fq.gz -G hg19 -O $$HOME/scratch -S atac_test --single-or-paired paired -R
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python $$CODEBASE/pepatac/pipelines/pepatac.py -I $$MICROTEST/data/atacR1.fq.gz -I2 $$MICROTEST/data/atacR2.fq.gz -G hg19 -O $$HOME/scratch -S atac_test --single-or-paired paired -R
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test:
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python pipelines/ATACseq.py -P 3 -M 100 -O test_out -R -S liver -G hg19 -Q paired -C ATACseq.yaml --genome-size hs --prealignments rCRSd human_repeats -I examples/test_data/liver-CD31_test_R1.fastq.gz -I2 examples/test_data/liver-CD31_test_R2.fastq.gz
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python pipelines/pepatac.py -P 3 -M 100 -O test_out -R -S liver -G hg19 -Q paired -C pepatac.yaml --genome-size hs --prealignments rCRSd human_repeats -I examples/test_data/liver-CD31_test_R1.fastq.gz -I2 examples/test_data/liver-CD31_test_R2.fastq.gz
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changtest:
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python pipelines/ATACseq.py -P 3 -M 100 -O test_out -R -S liver -G hg19 -Q paired -C $HOME/code/ATACseq/examples/chang_project/ATACseq.yaml -gs mm -I examples/test_data/liver-CD31_test_R1.fastq.gz -I2 examples/test_data/liver-CD31_test_R2.fastq.gz
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python pipelines/pepatac.py -P 3 -M 100 -O test_out -R -S liver -G hg19 -Q paired -C $HOME/code/pepatac/examples/chang_project/pepatac.yaml -gs mm -I examples/test_data/liver-CD31_test_R1.fastq.gz -I2 examples/test_data/liver-CD31_test_R2.fastq.gz
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docker:
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docker build -t databio/pepatac -f containers/pepatac.Dockerfile .
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singularity:
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singularity build $${SIMAGES}pepatac docker://databio/pepatac

‎README.md‎

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‎config/pipeline_interface.yaml‎

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ATACseq.py:
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name: ATACseq
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pepatac.py:
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name: PEPATAC
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looper_args: True
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required_input_files: [read1, read2]
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all_input_files: [read1, read2]

‎config/protocol_mappings.yaml‎

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ATAC: ATACseq.py
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ATAC-SEQ: ATACseq.py
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ATAC: pepatac.py
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ATAC-SEQ: pepatac.py

‎containers/pepatac.Dockerfile‎

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# Pull base image
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FROM phusion/baseimage:0.10.1
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# Who maintains this image
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LABEL maintainer Jason Smith "[email protected]"
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# Version info
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LABEL version 0.8.1
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# Use baseimage-docker's init system.
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CMD ["/sbin/my_init"]
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# Install dependencies
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RUN apt-get update && \
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DEBIAN_FRONTEND=noninteractive apt-get install --assume-yes \
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curl \
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default-jre \
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default-jdk \
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git \
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libcommons-math3-java \
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libcurl4-gnutls-dev \
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libjbzip2-java \
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libpng-dev \
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libssl-dev \
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libtbb2 \
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libtbb-dev \
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openssl \
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pigz \
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python \
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python-pip python-dev build-essential \
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wget
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# Install MySQL server
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RUN DEBIAN_FRONTEND=noninteractive apt-get install --assume-yes mysql-server \
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mysql-client \
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libmysqlclient-dev
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# Install python tools
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RUN pip install --upgrade pip
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RUN pip install virtualenv && \
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pip install numpy && \
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pip install MACS2 && \
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pip install pararead && \
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pip install piper
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# Install R
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RUN DEBIAN_FRONTEND=noninteractive apt-get --assume-yes install r-base r-base-dev && \
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echo "r <- getOption('repos'); r['CRAN'] <- 'http://cran.us.r-project.org'; options(repos = r);" > ~/.Rprofile && \
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Rscript -e "install.packages('devtools')" && \
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Rscript -e "devtools::install_github('pepkit/pepr')" && \
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Rscript -e "install.packages('gtable')" && \
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Rscript -e "install.packages('argparser')" && \
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Rscript -e "install.packages('ggplot2')" && \
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Rscript -e "install.packages('gplots')" && \
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Rscript -e "install.packages('grid')" && \
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Rscript -e "install.packages('scales')" && \
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Rscript -e "install.packages('data.table')" && \
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Rscript -e "install.packages('stringr')"
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# Install bedtools
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RUN DEBIAN_FRONTEND=noninteractive apt-get install --assume-yes \
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ant \
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bedtools
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# Install fastqc
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WORKDIR /home/tools/
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RUN wget http://www.bioinformatics.babraham.ac.uk/projects/fastqc/fastqc_v0.11.7.zip && \
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unzip fastqc_v0.11.7.zip && \
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cd /home/tools/FastQC && \
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chmod 755 fastqc && \
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ln -s /home/tools/FastQC/fastqc /usr/bin/
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# Install htslib
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WORKDIR /home/src/
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RUN wget https://github.com/samtools/htslib/releases/download/1.7/htslib-1.7.tar.bz2 && \
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tar xf htslib-1.7.tar.bz2 && \
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cd /home/src/htslib-1.7 && \
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./configure --prefix /home/tools/ && \
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make && \
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make install
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# Install samtools
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WORKDIR /home/src/
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RUN wget https://github.com/samtools/samtools/releases/download/1.7/samtools-1.7.tar.bz2 && \
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tar xf samtools-1.7.tar.bz2 && \
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cd /home/src/samtools-1.7 && \
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./configure && \
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make && \
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make install && \
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ln -s /home/src/samtools-1.7/samtools /usr/bin/
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# Install bowtie2
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WORKDIR /home/src/
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RUN wget https://downloads.sourceforge.net/project/bowtie-bio/bowtie2/2.3.4.1/bowtie2-2.3.4.1-source.zip && \
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unzip bowtie2-2.3.4.1-source.zip && \
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cd /home/src/bowtie2-2.3.4.1 && \
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make && \
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make install && \
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ln -s /home/src/bowtie2-2.3.4.1/bowtie2 /usr/bin/
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# Install picard
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WORKDIR /home/tools/bin
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RUN wget https://github.com/broadinstitute/picard/releases/download/2.18.0/picard.jar && \
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chmod +x picard.jar
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# Install UCSC tools
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WORKDIR /home/tools/
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RUN wget http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64/bedGraphToBigWig && \
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wget http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64/wigToBigWig && \
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wget http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64/bigWigCat && \
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wget http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/bedSort && \
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chmod +x /home/tools/bedGraphToBigWig && \
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chmod +x /home/tools/wigToBigWig && \
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chmod +x /home/tools/bigWigCat && \
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chmod +x /home/tools/bedSort && \
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ln -s /home/tools/bedGraphToBigWig /usr/bin/ && \
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ln -s /home/tools/wigToBigWig /usr/bin/ && \
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ln -s /home/tools/bigWigCat /usr/bin/ && \
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ln -s /home/tools/bedSort /usr/bin/
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# Install Skewer
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WORKDIR /home/src/
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RUN git clone git://github.com/relipmoc/skewer.git && \
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cd /home/src/skewer && \
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make && \
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make install
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# OPTIONAL REQUIREMENTS
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# Install F-seq
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WORKDIR /home/src/
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RUN wget https://github.com/aboyle/F-seq/archive/master.zip && \
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unzip master.zip && \
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cd /home/src/F-seq-master && \
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ant && \
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cd dist~/ && \
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tar xf fseq.tgz && \
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ln -s /home/src/F-seq-master/dist~/fseq/bin/fseq /usr/bin/
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# Install Trimmomatic
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WORKDIR /home/src/
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RUN wget http://www.usadellab.org/cms/uploads/supplementary/Trimmomatic/Trimmomatic-0.36.zip && \
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unzip Trimmomatic-0.36.zip && \
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chmod +x Trimmomatic-0.36/trimmomatic-0.36.jar
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# Set environment variables
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ENV PATH=/home/tools/bin:/home/tools/:/home/tools/bin/kentUtils/:/home/src/F-seq-master/dist~/fseq/bin:/home/src/bowtie2-2.3.4.1:/home/src/skewer:/home/src/samtools-1.7:/home/src/Trimmomatic-0.36/:/home/src/htslib-1.7:$PATH \
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TRIMMOMATIC=/home/src/Trimmomatic-0.36/trimmomatic-0.36.jar \
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PICARD=/home/tools/bin/picard.jar \
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R_LIBS_USER=/usr/local/lib/R/site-library/
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# Define default command
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WORKDIR /home/
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CMD ["/bin/bash"]
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# Clean up APT when done.
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RUN apt-get clean && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*

‎example_cmd.txt‎

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# Example commands of using pepATAC through pypiper.
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# For the example commands of using pepATAC with looper, please see the xxx Users Guide.
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# Example commands of using PEPATAC through pypiper.
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# For the example commands of using PEPATAC with looper, please see the xxx Users Guide.
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INPUT=/path/to/sequencing_results/fastq_files
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# run pepATAC on a human paired-end reads dataset using 5 threads:
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python pipelines/ATACseq.py -P 5 -O output_folder -S output_sample_name -G hg38 -Q paired -C ATACseq.yaml -gs hs -I $INPUT/ATACseq_results_PE_R1.fastq.gz -I2 $INPUT/ATACseq_results_PE_R2.fastq.gz
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# run PEPATAC on a human paired-end reads dataset using 5 threads:
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python pipelines/pepatac.py -P 5 -O output_folder -S output_sample_name -G hg38 -Q paired -C pepatac.yaml -gs hs -I $INPUT/pepatac_results_PE_R1.fastq.gz -I2 $INPUT/pepatac_results_PE_R2.fastq.gz
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# run pepATAC on multiple datasets at the same time: <- this could be wrong as I don't see an explaination of how to use -I and -I2 with multiple samples
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python pipelines/ATACseq.py -P 5 -O output_folder -S output_sample_name -G hg38 -Q paired -C ATACseq.yaml -gs hs -I $INPUT/ATACseq_results1_PE_R1.fastq.gz $INPUT/ATACseq_results2_PE_R1.fastq.gz $INPUT/ATACseq_results3_PE_R1.fastq.gz -I2 $INPUT/ATACseq_results1_PE_R2.fastq.gz $INPUT/ATACseq_results2_PE_R2.fastq.gz $INPUT/ATACseq_results3_PE_R2.fastq.gz
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# run PEPATAC on multiple datasets at the same time: <- this could be wrong as I don't see an explaination of how to use -I and -I2 with multiple samples
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python pipelines/pepatac.py -P 5 -O output_folder -S output_sample_name -G hg38 -Q paired -C pepatac.yaml -gs hs -I $INPUT/pepatac_results1_PE_R1.fastq.gz $INPUT/pepatac_results2_PE_R1.fastq.gz $INPUT/pepatac_results3_PE_R1.fastq.gz -I2 $INPUT/pepatac_results1_PE_R2.fastq.gz $INPUT/pepatac_results2_PE_R2.fastq.gz $INPUT/pepatac_results3_PE_R2.fastq.gz
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# run multiple samples with a for loop:
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declare -a sample_name_arr=("sample1","sample2","sample3")
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for sample_name in "${sample_name_arr[@]}"
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do
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file1=$INPUT/{$file1}_PE_R1.fastq.gz
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file2=${file1/R1/R2}
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python pipelines/ATACseq.py -P 5 -O output_folder -S $sample_name -G hg38 -Q paired -C ATACseq.yaml -gs hs -I $file1 -I2 $file2
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python pipelines/pepatac.py -P 5 -O output_folder -S $sample_name -G hg38 -Q paired -C pepatac.yaml -gs hs -I $file1 -I2 $file2
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done
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# run pepATAC on a mouse single-end reads dataset using 8 threads:
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python pipelines/ATACseq.py -P 8 -O output_folder -S output_sample_name -G mm10 -Q single -C ATACseq.yaml -gs mm -I $INPUT/ATACseq_results_PE_R1.fastq.gz
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# run PEPATAC on a mouse single-end reads dataset using 8 threads:
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python pipelines/pepatac.py -P 8 -O output_folder -S output_sample_name -G mm10 -Q single -C pepatac.yaml -gs mm -I $INPUT/pepatac_results_PE_R1.fastq.gz
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# run pepATAC with different trimming tools then default trimmomatic, currectly supports skewer and pyadapt:
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python pipelines/ATACseq.py --skewer TRUE -P 5 -O output_folder -S output_sample_name -G hg38 -Q paired -C ATACseq.yaml -gs hs -I $INPUT/ATACseq_results_PE_R1.fastq.gz -I2 $INPUT/ATACseq_results_PE_R2.fastq.gz
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python pipelines/ATACseq.py --pyadapt TRUE -P 5 -O output_folder -S output_sample_name -G hg38 -Q paired -C ATACseq.yaml -gs hs -I $INPUT/ATACseq_results_PE_R1.fastq.gz -I2 $INPUT/ATACseq_results_PE_R2.fastq.gz
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# re-run pepATAC and over-write the previous output:
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python pipelines/ATACseq.py -N -P 5 -O output_folder -S output_sample_name -G hg38 -Q paired -C ATACseq.yaml -gs hs -I $INPUT/ATACseq_results_PE_R1.fastq.gz -I2 $INPUT/ATACseq_results_PE_R2.fastq.gz
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# continue to run pepATAC since a locked step (usually locked due to failure):
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python pipelines/ATACseq.py -R -P 5 -O output_folder -S output_sample_name -G hg38 -Q paired -C ATACseq.yaml -gs hs -I $INPUT/ATACseq_results_PE_R1.fastq.gz -I2 $INPUT/ATACseq_results_PE_R2.fastq.gz
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# check xxxx for full list of parameter usage
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# full list of parameters are listed below:
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python ATACseq.py
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usage: ATACseq.py [-h] [-N] [-I2 INPUT_FILES2 [INPUT_FILES2 ...]]
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[-M MEMORY_LIMIT] [-Q SINGLE_OR_PAIRED] [-S SAMPLE_NAME]
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[-P NUMBER_OF_CORES] [-D] [-I INPUT_FILES [INPUT_FILES ...]]
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[-F] [-R] [-C CONFIG_FILE] [-O PARENT_OUTPUT_FOLDER]
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[-G GENOME_ASSEMBLY] [-gs GENOME_SIZE]
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[--frip-ref-peaks FRIP_REF_PEAKS] [--pyadapt] [--skewer]
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[--prealignments PREALIGNMENTS [PREALIGNMENTS ...]] [-V]
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Pipeline
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optional arguments:
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-C CONFIG_FILE, --config CONFIG_FILE
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pipeline config file in YAML format; relative paths
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are considered relative to the pipeline script.
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defaults to ATACseq.yaml
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-D, --dirty Make all cleanups manual
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-F, --follow Run all follow commands, even if command is not run
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--frip-ref-peaks FRIP_REF_PEAKS
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Reference peak set for calculating FRIP
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-G GENOME_ASSEMBLY, --genome GENOME_ASSEMBLY
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identifier for genome assempbly (required)
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-gs GENOME_SIZE, --genome-size GENOME_SIZE
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genome size for MACS2
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-h, --help show this help message and exit
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-I INPUT_FILES [INPUT_FILES ...], --input INPUT_FILES [INPUT_FILES ...]
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One or more primary input files (required)
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-I2 INPUT_FILES2 [INPUT_FILES2 ...], --input2 INPUT_FILES2 [INPUT_FILES2 ...]
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One or more secondary input files (if they exists);
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for example, second read in pair.
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-M MEMORY_LIMIT, --mem MEMORY_LIMIT
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Memory string for processes that accept memory limits
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(like java)
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-N, --new-start Fresh start mode, overwrite all
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-O PARENT_OUTPUT_FOLDER, --output-parent PARENT_OUTPUT_FOLDER
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parent output directory of the project (required).
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-P NUMBER_OF_CORES, --cores NUMBER_OF_CORES
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number of cores to use for parallel processes
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-Q SINGLE_OR_PAIRED, --single-or-paired SINGLE_OR_PAIRED
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single or paired end? default: single
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-R, --recover Recover mode, overwrite locks
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-S SAMPLE_NAME, --sample-name SAMPLE_NAME
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unique name for output subfolder and files (required)
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--pyadapt Use pyadapter_trim for trimming? [Default: False]
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--skewer Use skewer for trimming? [Default: False]
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--prealignments PREALIGNMENTS [PREALIGNMENTS ...]
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List of reference genomes to align to before primary
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alignment.
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-V, --version show program's version number and exit'
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# run PEPATAC with different trimming tools then default trimmomatic, currectly supports skewer and pyadapt:
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python pipelines/pepatac.py --skewer TRUE -P 5 -O output_folder -S output_sample_name -G hg38 -Q paired -C pepatac.yaml -gs hs -I $INPUT/pepatac_results_PE_R1.fastq.gz -I2 $INPUT/pepatac_results_PE_R2.fastq.gz
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python pipelines/pepatac.py --pyadapt TRUE -P 5 -O output_folder -S output_sample_name -G hg38 -Q paired -C pepatac.yaml -gs hs -I $INPUT/pepatac_results_PE_R1.fastq.gz -I2 $INPUT/pepatac_results_PE_R2.fastq.gz
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# re-run PEPATAC and over-write the previous output:
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python pipelines/pepatac.py -N -P 5 -O output_folder -S output_sample_name -G hg38 -Q paired -C pepatac.yaml -gs hs -I $INPUT/pepatac_results_PE_R1.fastq.gz -I2 $INPUT/pepatac_results_PE_R2.fastq.gz
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# continue to run PEPATAC since a locked step (usually locked due to failure):
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python pipelines/pepatac.py -R -P 5 -O output_folder -S output_sample_name -G hg38 -Q paired -C pepatac.yaml -gs hs -I $INPUT/pepatac_results_PE_R1.fastq.gz -I2 $INPUT/pepatac_results_PE_R2.fastq.gz
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‎examples/chang_project/README.md‎

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This folder contains an skeleton template with configuration options already set for the Chang lab compute environment. To set up a new project in the Chang lab compute environment, follow these instructions:
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1. Follow the **installing** instructions in the main README to get prerequisites (install looper, pypiper, and clone the ATACseq repository).
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1. Follow the **installing** instructions in the main README to get prerequisites (install looper, pypiper, and clone the PEPATAC repository).
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2. Copy this folder ([examples/chang_project](examples/chang_project/)) and name the new folder for your project.
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3. In your new folder, edit `project_config.yaml` to set the `metadata.pipelines_dir` option to the location of your cloned ATACseq repository.
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3. In your new folder, edit `project_config.yaml` to set the `metadata.pipelines_dir` option to the location of your cloned PEPATAC repository.
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4. Edit `project_config.yaml` to set the `data_sources.R1` and `data_sources.R2` to point to where you store fastq files. Your files must be named in some systematic pattern that can be created by populating sample variables, like `{sample_name}`. Detailed instructions are available here: [using looper derived columns](http://looper.readthedocs.io/en/latest/advanced.html#pointing-to-flexible-data-with-derived-columns).
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5. Make any other (optional) changes you want to `project_config.yaml`.
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6. Modify `project_annotation.csv` to include your sample list.
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7. Run the project with `looper run path/to/project_config.yaml`.
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Essentially, all this does differently from the default is that we have provided a configuration file. See the `pipeline_config` section in the [project config file](examples/chang_project/project_config.yaml) -- we simply set this to `ATACseq_chang.yaml` for your project, and then include [ATACseq_chang.yaml](examples/chang_project/ATACseq_chang.yaml) parallel to the project config file.
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Essentially, all this does differently from the default is that we have provided a configuration file. See the `pipeline_config` section in the [project config file](examples/chang_project/project_config.yaml) -- we simply set this to `pepatac_chang.yaml` for your project, and then include [pepatac_chang.yaml](examples/chang_project/pepatac_chang.yaml) parallel to the project config file.
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Once you have it set up, you have all the power of looper for your project. It's simple to submit to a cluster, summarize your results, clean, and monitor your project. You can find additional details on what you can do with this in the [looper docs](http://looper.readthedocs.io/).

‎examples/chang_project/ATACseq_chang.yaml‎ renamed to ‎examples/chang_project/pepatac_chang.yaml‎

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# Configuration file for ATACseq pipeline based on pypiper
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# PEPATAC configuration file for an ATACseq pipeline based on pypiper
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# basic tools
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# public tools

‎examples/chang_project/project_config.yaml‎

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@@ -33,6 +33,6 @@ implied_columns:
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prealignments: null
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pipeline_config:
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ATACseq.py: ATACseq_chang.yaml # Use this to load Chang Lab settings
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#ATACseq.py: null # Use this to load default environment settings
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pepatac.py: pepatac_chang.yaml # Use this to load Chang Lab settings
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#pepatac.py: null # Use this to load default environment settings
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