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#FROM dhspence/docker-genomic-analysis:6
FROM johnegarza/genome-utils:v0.1
MAINTAINER David H. Spencer <dspencer@wustl.edu>
LABEL description="Heavy container for Chromoseq"
#
# install manta
#
ENV manta_version 1.5.0
WORKDIR /opt/
RUN wget https://github.com/Illumina/manta/releases/download/v${manta_version}/manta-${manta_version}.centos6_x86_64.tar.bz2 && \
tar -jxvf manta-${manta_version}.centos6_x86_64.tar.bz2 && \
mv manta-${manta_version}.centos6_x86_64 /usr/local/src/manta
#
# install hmmcopy and ichor
#
RUN apt-get update && \
apt-get install -y build-essential \
cmake \
python-dev \
python-pip \
git \
wget \
autoconf \
zlib1g-dev \
fort77 \
liblzma-dev \
libblas-dev \
gfortran \
gcc-multilib \
gobjc++ \
aptitude \
libreadline-dev \
python-dev \
libpcre3 \
libpcre3-dev \
default-jdk
ENV VARSCAN_INSTALL_DIR=/opt/varscan
WORKDIR $VARSCAN_INSTALL_DIR
RUN wget https://github.com/dkoboldt/varscan/releases/download/2.4.2/VarScan.v2.4.2.jar && \
ln -s VarScan.v2.4.2.jar VarScan.jar
#
# pindel
#
WORKDIR /opt
RUN wget https://github.com/samtools/samtools/releases/download/1.2/samtools-1.2.tar.bz2 && \
tar xvjf samtools-1.2.tar.bz2
WORKDIR /opt/samtools-1.2
RUN make
WORKDIR /opt
RUN wget https://github.com/genome/pindel/archive/v0.2.5b8.tar.gz && \
tar -xzf v0.2.5b8.tar.gz
WORKDIR /opt/pindel-0.2.5b8
RUN ./INSTALL /opt/samtools-1.2/htslib-1.2.1
WORKDIR /
RUN ln -s /opt/pindel-0.2.5b8/pindel /usr/local/bin/pindel && \
ln -s /opt/pindel-0.2.5b8/pindel2vcf /usr/local/bin/pindel2vcf
###############
# Octopus
###############
#RUN conda install -y -c conda-forge -c bioconda octopus
#
# GATK
#
#GATK 3.6#
ENV maven_package_name apache-maven-3.3.9
ENV gatk_dir_name gatk-protected
ENV gatk_version 3.6
RUN cd /tmp/ && wget -q http://mirror.nohup.it/apache/maven/maven-3/3.3.9/binaries/apache-maven-3.3.9-bin.zip
# LSF: Comment out the oracle.jrockit.jfr.StringConstantPool.
RUN cd /tmp/ \
&& git clone --recursive https://github.com/broadgsa/gatk-protected.git \
&& cd /tmp/gatk-protected && git checkout tags/${gatk_version} \
&& sed -i 's/^import oracle.jrockit.jfr.StringConstantPool;/\/\/import oracle.jrockit.jfr.StringConstantPool;/' ./public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/VariantEval.java \
&& mv /tmp/gatk-protected /opt/${gatk_dir_name}-${gatk_version}
RUN cd /opt/ && unzip /tmp/${maven_package_name}-bin.zip \
&& rm -rf /tmp/${maven_package_name}-bin.zip LICENSE NOTICE README.txt \
&& cd /opt/ \
&& cd /opt/${gatk_dir_name}-${gatk_version} && /opt/${maven_package_name}/bin/mvn verify -P\!queue \
&& mv /opt/${gatk_dir_name}-${gatk_version}/protected/gatk-package-distribution/target/gatk-package-distribution-${gatk_version}.jar /opt/GenomeAnalysisTK.jar \
&& rm -rf /opt/${gatk_dir_name}-${gatk_version} /opt/${maven_package_name}
#
# pysam and scipy
#
RUN conda config --add channels r && conda config --add channels bioconda && conda install -c conda-forge petl && \
conda install -c anaconda biopython && conda install -c anaconda scipy && conda install pysam
#
# blat
#
WORKDIR /usr/local/bin/
RUN wget http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64/blat/blat && \
chmod a+x blat
########
#VEP 90#
########
RUN cpan install DBI && cpan install Module::Build.pm
RUN mkdir /opt/vep/
WORKDIR /opt/vep
RUN git clone https://github.com/Ensembl/ensembl-vep.git
WORKDIR /opt/vep/ensembl-vep
RUN git checkout postreleasefix/90
RUN perl INSTALL.pl --NO_UPDATE
WORKDIR /
RUN ln -s /opt/vep/ensembl-vep/vep /usr/bin/variant_effect_predictor.pl
RUN conda install -y -c bioconda cyvcf2 htslib samtools deeptools mosdepth
RUN export PATH=$PATH:/opt/conda/bin/ && \
/bin/bash -c "source activate python2 && conda install -c bioconda svtools && source deactivate"
#
# Cleanup
#
## Clean up
RUN cd / && \
rm -rf /tmp/* && \
apt-get autoremove -y && \
apt-get autoclean -y && \
rm -rf /var/lib/apt/lists/* && \
apt-get clean && \
rm -f /opt/*.bz2 /opt/*.gz
RUN mkdir -p /opt/lib/perl/VEP/Plugins && chmod a+wrx /opt/lib/perl/VEP/Plugins
COPY Downstream.pm /opt/lib/perl/VEP/Plugins/Downstream.pm
COPY Wildtype.pm /opt/lib/perl/VEP/Plugins/Wildtype.pm
#install docker, instructions from https://docs.docker.com/install/linux/docker-ce/ubuntu/#install-using-the-repository
RUN apt-get update && apt-get install -y \
apt-transport-https \
ca-certificates \
curl \
gnupg-agent \
software-properties-common
RUN curl -fsSL https://download.docker.com/linux/ubuntu/gpg | apt-key add -
RUN add-apt-repository \
"deb [arch=amd64] https://download.docker.com/linux/ubuntu \
$(lsb_release -cs) \
stable"
RUN apt-get update
RUN apt-get install -y docker-ce
WORKDIR /opt/
RUN wget https://github.com/broadinstitute/cromwell/releases/download/36/cromwell-36.jar
RUN mkdir /opt/files/
COPY add_annotations_to_table_helper.py /usr/local/bin/add_annotations_to_table_helper.py
COPY docm_and_coding_indel_selection.pl /usr/local/bin/docm_and_coding_indel_selection.pl
COPY runIchorCNA.R /usr/local/bin/runIchorCNA.R
COPY addReadCountsToVcfCRAM.py /usr/local/bin/addReadCountsToVcfCRAM.py
COPY configManta.hg38.py.ini /opt/files/configManta.hg38.py.ini
COPY ChromoSeq.hg38.bed /opt/files/ChromoSeq.hg38.bed
COPY GeneRegions.bed /opt/files/GeneRegions.bed
COPY ChromoSeq.translocations.fixed.v3.sorted.hg38.bedpe /opt/files/ChromoSeq.translocations.fixed.v3.sorted.hg38.bedpe
COPY ChromoSeqReporter.hg38.pl /usr/local/bin/ChromoSeqReporter.hg38.pl
COPY BlatContigs.pl /usr/local/bin/BlatContigs.pl
COPY pslScore.pl /usr/local/bin/pslScore.pl
COPY hg38.blacklist.merged.bed /opt/files/hg38.blacklist.merged.bed
COPY B38.callset.public.bedpe.gz /opt/files/B38.callset.public.bedpe.gz
COPY all.stranded.filtered.merged.bedpe.gz /opt/files/all.stranded.filtered.merged.bedpe.gz
COPY all.stranded.filtered.merged.bedpe.gz.tbi /opt/files/all.stranded.filtered.merged.bedpe.gz.tbi
COPY GeneCoverageRegions.bed /opt/files/GeneCoverageRegions.bed
COPY ChromoSeq.translocations.qc.bed /opt/files/ChromoSeq.translocations.qc.bed
COPY nextera_hg38_500kb_median_normAutosome_median.rds_median.n9.rds /opt/files/nextera_hg38_500kb_median_normAutosome_median.rds_median.n9.rds
COPY basespace_cromwell.config /opt/files/basespace_cromwell.config
COPY Chromoseq_basespace.v9.wdl /opt/files/Chromoseq_basespace.v9.wdl
COPY all_sequences.dict /opt/files/all_sequences.dict
COPY all_sequences.fa.bed.gz /opt/files/all_sequences.fa.bed.gz
COPY all_sequences.fa.bed.gz.tbi /opt/files/all_sequences.fa.bed.gz.tbi
COPY all_sequences.fa.fai /opt/files/all_sequences.fa.fai
COPY driver.py /opt/files/driver.py
#RUN cd /opt/ && \
# git config --global http.sslVerify false && \
# git clone --recursive https://github.com/shahcompbio/hmmcopy_utils.git && \
# cd /opt/hmmcopy_utils && \
# cmake . && \
# make && \
# cp bin/* /usr/local/bin/
#RUN Rscript -e "source('https://bioconductor.org/biocLite.R'); biocLite('HMMcopy'); biocLite('GenomeInfoDb'); install.packages(c('devtools','optparse'))"
#RUN Rscript --default-packages=devtools -e "install_github('broadinstitute/ichorCNA')"
#RUN cd /opt/ && wget https://github.com/broadinstitute/ichorCNA/archive/master.zip && \
# unzip master.zip && mv ichorCNA-master/scripts/*.R /usr/local/bin/ && rm -Rf master.zip ichorCNA-master
#RUN Rscript -e "install.packages('devtools'); library('devtools'); install_github('broadinstitute/ichorCNA')"
RUN git clone https://github.com/broadinstitute/ichorCNA.git
RUN Rscript -e "install.packages(c('plyr', 'optparse')); source('https://bioconductor.org/biocLite.R'); biocLite('HMMcopy'); biocLite('GenomeInfoDb')"
RUN R CMD INSTALL ichorCNA
RUN chmod a+wrx /opt/files/*
RUN chmod a+wrx /usr/local/bin/*
#WORKDIR /opt/
#RUN conda install --yes 'pip' && \
# conda clean -tipsy && \
# pip install cmake==3.13
#RUN git clone -b master https://github.com/luntergroup/octopus.git && \
# cd octopus && \
# /opt/conda/bin/python ./scripts/install.py