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Merge pull request nf-core#1 from ewels/bioconda
WIP: Bioconda environment file.
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FROM openjdk:8 | ||
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||
LABEL author="Phil Ewels" \ | ||
description="Docker image containing all requirements for nf-core/ChIPseq pipeline" \ | ||
maintainer="[email protected]" | ||
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||
# Install container-wide requrements gcc, pip, zlib, libssl, make, libncurses, fortran77, g++, R | ||
RUN apt-get update && \ | ||
apt-get install -y --no-install-recommends \ | ||
g++ \ | ||
gawk \ | ||
gcc \ | ||
gfortran \ | ||
libboost-all-dev \ | ||
libbz2-dev \ | ||
libcurl4-openssl-dev \ | ||
libdbd-mysql \ | ||
libgsl0-dev \ | ||
liblzma-dev \ | ||
libmariadb-client-lgpl-dev \ | ||
libncurses5-dev \ | ||
libpcre3-dev \ | ||
libreadline-dev \ | ||
libssl-dev \ | ||
libxml2-dev \ | ||
make \ | ||
python-dev \ | ||
zlib1g-dev \ | ||
&& rm -rf /var/lib/apt/lists/* | ||
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# Use gawk instead of awk (needed for phantompeakqualtools) | ||
RUN update-alternatives --set awk /usr/bin/gawk | ||
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# Install pip | ||
RUN curl -fsSL https://bootstrap.pypa.io/get-pip.py -o /opt/get-pip.py && \ | ||
python /opt/get-pip.py && \ | ||
rm /opt/get-pip.py | ||
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# Install FastQC | ||
ENV FASTQC_BIN="fastqc_v0.11.5.zip" | ||
RUN curl -fsSL http://www.bioinformatics.babraham.ac.uk/projects/fastqc/$FASTQC_BIN -o /opt/$FASTQC_BIN && \ | ||
unzip /opt/$FASTQC_BIN -d /opt/ && \ | ||
chmod 755 /opt/FastQC/fastqc && \ | ||
ln -s /opt/FastQC/fastqc /usr/local/bin/fastqc && \ | ||
rm /opt/$FASTQC_BIN | ||
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# Install cutadapt | ||
RUN pip install cutadapt | ||
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# Install TrimGalore | ||
ENV TRIMGALORE_VERSION="0.4.5" | ||
RUN curl -fsSL https://github.com/FelixKrueger/TrimGalore/archive/${TRIMGALORE_VERSION}.tar.gz -o /opt/trimgalore_${TRIMGALORE_VERSION}.tar.gz && \ | ||
tar xvzf /opt/trimgalore_${TRIMGALORE_VERSION}.tar.gz -C /opt/ && \ | ||
ln -s /opt/TrimGalore-${TRIMGALORE_VERSION}/trim_galore /usr/local/bin/trim_galore && \ | ||
rm /opt/trimgalore_${TRIMGALORE_VERSION}.tar.gz | ||
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# Install BWA | ||
ENV BWA_VERSION="0.7.15" | ||
RUN curl -fsSL https://downloads.sourceforge.net/project/bio-bwa/bwa-${BWA_VERSION}.tar.bz2 -o /opt/bwa-${BWA_VERSION}.tar.bz2 && \ | ||
tar xvjf /opt/bwa-${BWA_VERSION}.tar.bz2 -C /opt/ && \ | ||
cd /opt/bwa-${BWA_VERSION};make && \ | ||
ln -s /opt/bwa-${BWA_VERSION}/bwa /usr/local/bin/bwa && \ | ||
rm /opt/bwa-${BWA_VERSION}.tar.bz2 | ||
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# Install SAMTools | ||
ENV SAMTOOLS_VERSON="1.6" | ||
RUN curl -fsSL https://github.com/samtools/samtools/releases/download/${SAMTOOLS_VERSON}/samtools-${SAMTOOLS_VERSON}.tar.bz2 -o /opt/samtools-${SAMTOOLS_VERSON}.tar.bz2 && \ | ||
tar xvjf /opt/samtools-${SAMTOOLS_VERSON}.tar.bz2 -C /opt/ && \ | ||
cd /opt/samtools-${SAMTOOLS_VERSON};make;make install && \ | ||
rm /opt/samtools-${SAMTOOLS_VERSON}.tar.bz2 | ||
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# Install PicardTools | ||
ENV PICARD_VERSION="picard-tools-2.0.1" | ||
RUN curl -fsSL https://github.com/broadinstitute/picard/releases/download/2.0.1/${PICARD_VERSION}.zip -o /opt/${PICARD_VERSION}.zip && \ | ||
unzip /opt/${PICARD_VERSION}.zip -d /opt/ && \ | ||
rm /opt/${PICARD_VERSION}.zip | ||
ENV PICARD_HOME /opt/${PICARD_VERSION} | ||
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# Install BEDTools | ||
ENV BEDTOOLS_VERSION="bedtools-2.26.0" | ||
RUN curl -fsSL https://github.com/arq5x/bedtools2/releases/download/v2.26.0/${BEDTOOLS_VERSION}.tar.gz -o /opt/${BEDTOOLS_VERSION}.tar.gz && \ | ||
tar xvzf /opt/${BEDTOOLS_VERSION}.tar.gz -C /opt/ && \ | ||
cd /opt/bedtools2; make && \ | ||
cp /opt/bedtools2/bin/* /usr/local/bin/ && \ | ||
rm /opt/${BEDTOOLS_VERSION}.tar.gz | ||
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# Install R | ||
ENV R_VERSION="R-3.4.2" | ||
RUN curl -fsSL https://cran.r-project.org/src/base/R-3/${R_VERSION}.tar.gz -o /opt/${R_VERSION}.tar.gz && \ | ||
tar xvzf /opt/${R_VERSION}.tar.gz -C /opt/ && \ | ||
cd /opt/${R_VERSION};./configure;make;make install && \ | ||
rm /opt/${R_VERSION}.tar.gz | ||
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# Install core R dependencies | ||
RUN echo "r <- getOption('repos'); r['CRAN'] <- 'https://ftp.acc.umu.se/mirror/CRAN/'; options(repos = r);" > ~/.Rprofile && \ | ||
Rscript -e "install.packages('caTools',dependencies=TRUE)" && \ | ||
Rscript -e "install.packages('snow',dependencies=TRUE)" && \ | ||
Rscript -e "install.packages('doMC',dependencies=TRUE)" && \ | ||
Rscript -e "install.packages('utils',dependencies=TRUE)" && \ | ||
Rscript -e "install.packages('stringr',dependencies=TRUE)" && \ | ||
Rscript -e "install.packages('markdown',dependencies=TRUE)" && \ | ||
Rscript -e "install.packages('evaluate',dependencies=TRUE)" && \ | ||
Rscript -e "install.packages('ggplot2',dependencies=TRUE)" && \ | ||
Rscript -e "install.packages('knitr',dependencies=TRUE)" && \ | ||
Rscript -e "install.packages('RMySQL',dependencies=TRUE)" | ||
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# Install R Bioconductor packages | ||
RUN echo 'source("https://bioconductor.org/biocLite.R")' > /opt/packages.r && \ | ||
echo 'biocLite()' >> /opt/packages.r && \ | ||
echo 'biocLite(c("BSgenome", "Rsamtools", "ShortRead", "GenomicRanges", "GenomicFeatures", "ensembldb", "ChIPpeakAnno", "biomaRt", "rtracklayer", "BSgenome.Hsapiens.UCSC.hg19", "org.Hs.eg.db", "BSgenome.Mmusculus.UCSC.mm10", "org.Mm.eg.db"))' >> /opt/packages.r && \ | ||
Rscript /opt/packages.r && \ | ||
mkdir /usr/local/lib/R/site-library | ||
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# Install phantompeakqualtools | ||
ENV SPP_VERSION="1.15" | ||
ENV PHANTOMPEAKQUALTOOLS_VERSION="v.1.1" | ||
RUN curl -fsSL https://github.com/hms-dbmi/spp/archive/${SPP_VERSION}.tar.gz -o /opt/SPP_${SPP_VERSION}.tar.gz && \ | ||
Rscript -e "install.packages('/opt/SPP_${SPP_VERSION}.tar.gz',dependencies=TRUE)" && \ | ||
rm /opt/SPP_${SPP_VERSION}.tar.gz && \ | ||
curl -fsSL https://storage.googleapis.com/google-code-archive-downloads/v2/code.google.com/phantompeakqualtools/ccQualityControl.${PHANTOMPEAKQUALTOOLS_VERSION}.tar.gz -o /opt/phantompeakqualtools.${PHANTOMPEAKQUALTOOLS_VERSION}.tar.gz && \ | ||
tar xvzf /opt/phantompeakqualtools.${PHANTOMPEAKQUALTOOLS_VERSION}.tar.gz -C /opt/ && \ | ||
chmod 755 /opt/phantompeakqualtools/* && \ | ||
echo 'alias run_spp.R="Rscript /opt/phantompeakqualtools/run_spp.R"' >> ~/.bashrc && \ | ||
rm /opt/phantompeakqualtools.${PHANTOMPEAKQUALTOOLS_VERSION}.tar.gz | ||
ENV PATH=${PATH}:/opt/phantompeakqualtools | ||
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# Install DeepTools | ||
ENV DEEPTOOLS_VERSION="2.5.4" | ||
RUN pip install git+git://github.com/fidelram/deepTools.git@$DEEPTOOLS_VERSION | ||
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# Install ngsplot | ||
ENV NGSPLOT_VERSION="2.63" | ||
RUN curl -fsSL https://github.com/shenlab-sinai/ngsplot/archive/${NGSPLOT_VERSION}.tar.gz -o /opt/ngsplot_${NGSPLOT_VERSION}.tar.gz && \ | ||
tar xvzf /opt/ngsplot_${NGSPLOT_VERSION}.tar.gz -C /opt/ && \ | ||
rm /opt/ngsplot_${NGSPLOT_VERSION}.tar.gz | ||
ENV PATH=${PATH}:/opt/ngsplot-${NGSPLOT_VERSION}/bin | ||
ENV NGSPLOT=/opt/ngsplot-${NGSPLOT_VERSION}/ | ||
RUN curl -fsSL https://export.uppmax.uu.se/b2013064/test-data/nfcore-chipseq_test_set.tar.bz2 -o /opt/nfcore-chipseq_test_set.tar.bz2 && \ | ||
tar xvjf /opt/nfcore-chipseq_test_set.tar.bz2 -C /opt/ && \ | ||
echo y | ngsplotdb.py install /opt/nfcore-chipseq_test_set/ngsplotdb_mm10_75_3.00.tar.gz && \ | ||
echo y | ngsplotdb.py install /opt/nfcore-chipseq_test_set/ngsplotdb_hg19_75_3.00.tar.gz && \ | ||
rm /opt/nfcore-chipseq_test_set.tar.bz2 && \ | ||
rm -rf /opt/nfcore-chipseq_test_set | ||
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# Install MACS | ||
RUN pip install MACS2 | ||
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# Install MultiQC | ||
ENV MULTIQC_VERSION="v1.4" | ||
RUN pip install git+git://github.com/ewels/MultiQC.git@$MULTIQC_VERSION | ||
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# Create root directories for UPPMAX and c3se hebbe | ||
RUN mkdir /pica /lupus /crex1 /crex2 /proj /scratch /sw \ | ||
/c3se /local /apps | ||
FROM nfcore/base | ||
MAINTAINER Phil Ewels <[email protected]> | ||
LABEL authors="[email protected]" \ | ||
description="Docker image containing all requirements for the nfcore/ChIPseq pipeline" | ||
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COPY environment.yml / | ||
RUN conda env create -f /environment.yml && conda clean -a | ||
ENV PATH /opt/conda/envs/nfcore-chipseq-1.4dev/bin:$PATH |
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FROM openjdk:8 | ||
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LABEL author="Phil Ewels" \ | ||
description="Docker image containing all requirements for nf-core/ChIPseq pipeline" \ | ||
maintainer="[email protected]" | ||
|
||
# Install container-wide requrements gcc, pip, zlib, libssl, make, libncurses, fortran77, g++, R | ||
RUN apt-get update && \ | ||
apt-get install -y --no-install-recommends \ | ||
g++ \ | ||
gawk \ | ||
gcc \ | ||
gfortran \ | ||
libboost-all-dev \ | ||
libbz2-dev \ | ||
libcurl4-openssl-dev \ | ||
libdbd-mysql \ | ||
libgsl0-dev \ | ||
liblzma-dev \ | ||
libmariadb-client-lgpl-dev \ | ||
libncurses5-dev \ | ||
libpcre3-dev \ | ||
libreadline-dev \ | ||
libssl-dev \ | ||
libxml2-dev \ | ||
make \ | ||
python-dev \ | ||
zlib1g-dev \ | ||
&& rm -rf /var/lib/apt/lists/* | ||
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# Use gawk instead of awk (needed for phantompeakqualtools) | ||
RUN update-alternatives --set awk /usr/bin/gawk | ||
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# Install pip | ||
RUN curl -fsSL https://bootstrap.pypa.io/get-pip.py -o /opt/get-pip.py && \ | ||
python /opt/get-pip.py && \ | ||
rm /opt/get-pip.py | ||
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# Install FastQC | ||
ENV FASTQC_BIN="fastqc_v0.11.5.zip" | ||
RUN curl -fsSL http://www.bioinformatics.babraham.ac.uk/projects/fastqc/$FASTQC_BIN -o /opt/$FASTQC_BIN && \ | ||
unzip /opt/$FASTQC_BIN -d /opt/ && \ | ||
chmod 755 /opt/FastQC/fastqc && \ | ||
ln -s /opt/FastQC/fastqc /usr/local/bin/fastqc && \ | ||
rm /opt/$FASTQC_BIN | ||
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# Install cutadapt | ||
RUN pip install cutadapt | ||
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# Install TrimGalore | ||
ENV TRIMGALORE_VERSION="0.4.5" | ||
RUN curl -fsSL https://github.com/FelixKrueger/TrimGalore/archive/${TRIMGALORE_VERSION}.tar.gz -o /opt/trimgalore_${TRIMGALORE_VERSION}.tar.gz && \ | ||
tar xvzf /opt/trimgalore_${TRIMGALORE_VERSION}.tar.gz -C /opt/ && \ | ||
ln -s /opt/TrimGalore-${TRIMGALORE_VERSION}/trim_galore /usr/local/bin/trim_galore && \ | ||
rm /opt/trimgalore_${TRIMGALORE_VERSION}.tar.gz | ||
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# Install BWA | ||
ENV BWA_VERSION="0.7.15" | ||
RUN curl -fsSL https://downloads.sourceforge.net/project/bio-bwa/bwa-${BWA_VERSION}.tar.bz2 -o /opt/bwa-${BWA_VERSION}.tar.bz2 && \ | ||
tar xvjf /opt/bwa-${BWA_VERSION}.tar.bz2 -C /opt/ && \ | ||
cd /opt/bwa-${BWA_VERSION};make && \ | ||
ln -s /opt/bwa-${BWA_VERSION}/bwa /usr/local/bin/bwa && \ | ||
rm /opt/bwa-${BWA_VERSION}.tar.bz2 | ||
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# Install SAMTools | ||
ENV SAMTOOLS_VERSON="1.6" | ||
RUN curl -fsSL https://github.com/samtools/samtools/releases/download/${SAMTOOLS_VERSON}/samtools-${SAMTOOLS_VERSON}.tar.bz2 -o /opt/samtools-${SAMTOOLS_VERSON}.tar.bz2 && \ | ||
tar xvjf /opt/samtools-${SAMTOOLS_VERSON}.tar.bz2 -C /opt/ && \ | ||
cd /opt/samtools-${SAMTOOLS_VERSON};make;make install && \ | ||
rm /opt/samtools-${SAMTOOLS_VERSON}.tar.bz2 | ||
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# Install PicardTools | ||
ENV PICARD_VERSION="picard-tools-2.0.1" | ||
RUN curl -fsSL https://github.com/broadinstitute/picard/releases/download/2.0.1/${PICARD_VERSION}.zip -o /opt/${PICARD_VERSION}.zip && \ | ||
unzip /opt/${PICARD_VERSION}.zip -d /opt/ && \ | ||
rm /opt/${PICARD_VERSION}.zip | ||
ENV PICARD_HOME /opt/${PICARD_VERSION} | ||
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# Install BEDTools | ||
ENV BEDTOOLS_VERSION="bedtools-2.26.0" | ||
RUN curl -fsSL https://github.com/arq5x/bedtools2/releases/download/v2.26.0/${BEDTOOLS_VERSION}.tar.gz -o /opt/${BEDTOOLS_VERSION}.tar.gz && \ | ||
tar xvzf /opt/${BEDTOOLS_VERSION}.tar.gz -C /opt/ && \ | ||
cd /opt/bedtools2; make && \ | ||
cp /opt/bedtools2/bin/* /usr/local/bin/ && \ | ||
rm /opt/${BEDTOOLS_VERSION}.tar.gz | ||
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# Install R | ||
ENV R_VERSION="R-3.4.2" | ||
RUN curl -fsSL https://cran.r-project.org/src/base/R-3/${R_VERSION}.tar.gz -o /opt/${R_VERSION}.tar.gz && \ | ||
tar xvzf /opt/${R_VERSION}.tar.gz -C /opt/ && \ | ||
cd /opt/${R_VERSION};./configure;make;make install && \ | ||
rm /opt/${R_VERSION}.tar.gz | ||
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||
# Install core R dependencies | ||
RUN echo "r <- getOption('repos'); r['CRAN'] <- 'https://ftp.acc.umu.se/mirror/CRAN/'; options(repos = r);" > ~/.Rprofile && \ | ||
Rscript -e "install.packages('caTools',dependencies=TRUE)" && \ | ||
Rscript -e "install.packages('snow',dependencies=TRUE)" && \ | ||
Rscript -e "install.packages('doMC',dependencies=TRUE)" && \ | ||
Rscript -e "install.packages('utils',dependencies=TRUE)" && \ | ||
Rscript -e "install.packages('stringr',dependencies=TRUE)" && \ | ||
Rscript -e "install.packages('markdown',dependencies=TRUE)" && \ | ||
Rscript -e "install.packages('evaluate',dependencies=TRUE)" && \ | ||
Rscript -e "install.packages('ggplot2',dependencies=TRUE)" && \ | ||
Rscript -e "install.packages('knitr',dependencies=TRUE)" && \ | ||
Rscript -e "install.packages('RMySQL',dependencies=TRUE)" | ||
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# Install R Bioconductor packages | ||
RUN echo 'source("https://bioconductor.org/biocLite.R")' > /opt/packages.r && \ | ||
echo 'biocLite()' >> /opt/packages.r && \ | ||
echo 'biocLite(c("BSgenome", "Rsamtools", "ShortRead", "GenomicRanges", "GenomicFeatures", "ensembldb", "ChIPpeakAnno", "biomaRt", "rtracklayer", "BSgenome.Hsapiens.UCSC.hg19", "org.Hs.eg.db", "BSgenome.Mmusculus.UCSC.mm10", "org.Mm.eg.db"))' >> /opt/packages.r && \ | ||
Rscript /opt/packages.r && \ | ||
mkdir /usr/local/lib/R/site-library | ||
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||
# Install phantompeakqualtools | ||
ENV SPP_VERSION="1.15" | ||
ENV PHANTOMPEAKQUALTOOLS_VERSION="v.1.1" | ||
RUN curl -fsSL https://github.com/hms-dbmi/spp/archive/${SPP_VERSION}.tar.gz -o /opt/SPP_${SPP_VERSION}.tar.gz && \ | ||
Rscript -e "install.packages('/opt/SPP_${SPP_VERSION}.tar.gz',dependencies=TRUE)" && \ | ||
rm /opt/SPP_${SPP_VERSION}.tar.gz && \ | ||
curl -fsSL https://storage.googleapis.com/google-code-archive-downloads/v2/code.google.com/phantompeakqualtools/ccQualityControl.${PHANTOMPEAKQUALTOOLS_VERSION}.tar.gz -o /opt/phantompeakqualtools.${PHANTOMPEAKQUALTOOLS_VERSION}.tar.gz && \ | ||
tar xvzf /opt/phantompeakqualtools.${PHANTOMPEAKQUALTOOLS_VERSION}.tar.gz -C /opt/ && \ | ||
chmod 755 /opt/phantompeakqualtools/* && \ | ||
echo 'alias run_spp.R="Rscript /opt/phantompeakqualtools/run_spp.R"' >> ~/.bashrc && \ | ||
rm /opt/phantompeakqualtools.${PHANTOMPEAKQUALTOOLS_VERSION}.tar.gz | ||
ENV PATH=${PATH}:/opt/phantompeakqualtools | ||
|
||
# Install DeepTools | ||
ENV DEEPTOOLS_VERSION="2.5.4" | ||
RUN pip install git+git://github.com/fidelram/deepTools.git@$DEEPTOOLS_VERSION | ||
|
||
# Install ngsplot | ||
ENV NGSPLOT_VERSION="2.63" | ||
RUN curl -fsSL https://github.com/shenlab-sinai/ngsplot/archive/${NGSPLOT_VERSION}.tar.gz -o /opt/ngsplot_${NGSPLOT_VERSION}.tar.gz && \ | ||
tar xvzf /opt/ngsplot_${NGSPLOT_VERSION}.tar.gz -C /opt/ && \ | ||
rm /opt/ngsplot_${NGSPLOT_VERSION}.tar.gz | ||
ENV PATH=${PATH}:/opt/ngsplot-${NGSPLOT_VERSION}/bin | ||
ENV NGSPLOT=/opt/ngsplot-${NGSPLOT_VERSION}/ | ||
RUN curl -fsSL https://export.uppmax.uu.se/b2013064/test-data/nfcore-chipseq_test_set.tar.bz2 -o /opt/nfcore-chipseq_test_set.tar.bz2 && \ | ||
tar xvjf /opt/nfcore-chipseq_test_set.tar.bz2 -C /opt/ && \ | ||
echo y | ngsplotdb.py install /opt/nfcore-chipseq_test_set/ngsplotdb_mm10_75_3.00.tar.gz && \ | ||
echo y | ngsplotdb.py install /opt/nfcore-chipseq_test_set/ngsplotdb_hg19_75_3.00.tar.gz && \ | ||
rm /opt/nfcore-chipseq_test_set.tar.bz2 && \ | ||
rm -rf /opt/nfcore-chipseq_test_set | ||
|
||
# Install MACS | ||
RUN pip install MACS2 | ||
|
||
# Install MultiQC | ||
ENV MULTIQC_VERSION="v1.4" | ||
RUN pip install git+git://github.com/ewels/MultiQC.git@$MULTIQC_VERSION |
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# You can use this file to create a conda environment for this pipeline: | ||
# conda env create -f environment.yml | ||
name: nfcore-chipseq-1.4dev | ||
channels: | ||
- bioconda | ||
- conda-forge | ||
- defaults | ||
dependencies: | ||
- conda-forge::openjdk=8.0.144 # Needed for FastQC - conda build hangs without this | ||
- fastqc=0.11.7 | ||
- trim-galore=0.4.5 | ||
- bwa=0.7.17 | ||
- conda-forge::r-markdown=0.8 | ||
- bioconda::r-spp=1.15.2 | ||
- bedtools=2.27.1 | ||
- samtools=1.8 | ||
- picard=2.18.2 | ||
- deeptools=3.0.2 | ||
- macs2=2.1.1 | ||
- multiqc=1.5 | ||
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||
# TODO: | ||
# - phantompeakqualtools | ||
# - R: caTools | ||
# - R: snow | ||
# - R: doMC | ||
# - R: utils | ||
# - R: stringr | ||
# - R: markdown | ||
# - R: evaluate | ||
# - R: ggplot2 | ||
# - R: knitr | ||
# - R: RMySQL | ||
# - Bioconductor: BSgenome | ||
# - Bioconductor: Rsamtools | ||
# - Bioconductor: ShortRead | ||
# - Bioconductor: GenomicRanges | ||
# - Bioconductor: GenomicFeatures | ||
# - Bioconductor: ensembldb | ||
# - Bioconductor: ChIPpeakAnno | ||
# - Bioconductor: biomaRt | ||
# - Bioconductor: rtracklayer | ||
# - Bioconductor: BSgenome.Hsapiens.UCSC.hg19 | ||
# - Bioconductor: org.Hs.eg.db | ||
# - Bioconductor: BSgenome.Mmusculus.UCSC.mm10 | ||
# - Bioconductor: org.Mm.eg.db |