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Dockerfile
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FROM ubuntu:20.04
MAINTAINER bhaas@broadinstitute.org
ENV DEBIAN_FRONTEND=noninteractive
RUN apt-get --allow-releaseinfo-change update && apt-get -qq -y install --no-install-recommends \
automake \
build-essential \
bzip2 \
ca-certificates \
curl \
default-jre \
g++ \
gcc \
git \
libbz2-dev \
libdb-dev \
liblzma-dev \
libssl-dev \
make \
pbzip2 \
perl \
pigz \
procps \
unzip \
wget \
zlib1g \
zlib1g-dev \
zlibc
RUN curl -L http://cpanmin.us | perl - App::cpanminus
RUN cpanm install URI::Escape
ENV SRC /usr/local/src
ENV BIN /usr/local/bin
# Install Miniconda
RUN apt-get update && apt-get install -y wget && rm -rf /var/lib/apt/lists/*
WORKDIR $SRC
RUN wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh -O miniconda_install.sh && \
bash ./miniconda_install.sh -b -p $BIN/miniconda3
ENV PATH="$BIN/miniconda3/bin:${PATH}"
RUN conda install python=3.10.12
RUN conda install -y pip && pip install requests pandas xgboost statsmodels ngboost scikit-learn
RUN pip install open-cravat==2.1.0
# Run an oc command to generate config files
RUN oc config md > /dev/null
## gatk
WORKDIR $SRC
ENV GATK_VERSION=4.1.9.0
RUN wget -q https://github.com/broadinstitute/gatk/releases/download/${GATK_VERSION}/gatk-${GATK_VERSION}.zip && \
unzip gatk-${GATK_VERSION}.zip && \
rm $SRC/gatk-${GATK_VERSION}.zip
ENV GATK_HOME $SRC/gatk-${GATK_VERSION}
## Samtools
ENV SAMTOOLS_VERSION=1.9
WORKDIR $SRC
RUN SAMTOOLS_URL="https://github.com/samtools/samtools/releases/download/${SAMTOOLS_VERSION}/samtools-${SAMTOOLS_VERSION}.tar.bz2" && \
wget -q $SAMTOOLS_URL && \
tar xvf samtools-${SAMTOOLS_VERSION}.tar.bz2 && \
cd samtools-${SAMTOOLS_VERSION}/htslib-${SAMTOOLS_VERSION} && ./configure && make && make install && \
cd ../ && ./configure --without-curses && make && make install && \
rm $SRC/samtools-${SAMTOOLS_VERSION}.tar.bz2
## BCFtools
RUN wget -q https://github.com/samtools/bcftools/releases/download/1.9/bcftools-1.9.tar.bz2 && \
tar xvf bcftools-1.9.tar.bz2 && \
cd bcftools-1.9 && ./configure && make && make install && \
rm $SRC/bcftools-1.9.tar.bz2
## Bedtools
RUN wget -q https://github.com/arq5x/bedtools2/releases/download/v2.30.0/bedtools-2.30.0.tar.gz && \
tar -zxvf bedtools-2.30.0.tar.gz && \
cd bedtools2 && \
make && \
cp bin/* $BIN/ && \
rm $SRC/bedtools-2.30.0.tar.gz
# pblat
RUN wget -q https://github.com/icebert/pblat/archive/2.5.tar.gz && \
tar -zxvf 2.5.tar.gz && \
cd pblat-2.5 && \
make && \
cp pblat $BIN/ && \
rm $SRC/2.5.tar.gz
## update igv-reports to current bleeding edge
#WORKDIR $SRC
#ENV IGV_REPORTS_CO=1086ed7258c09bfe213836e2dc53b043c352a4a9
#RUN git clone https://github.com/igvteam/igv-reports.git && \
# cd igv-reports && \
# git checkout ${IGV_REPORTS_CO} && \
# pip install -e .
RUN pip install igv-reports==1.9.0
#RUN wget -q https://github.com/broadinstitute/cromwell/releases/download/58/cromwell-58.jar -O /usr/local/src/ctat-mutations/WDL/cromwell-58.jar
#RUN wget -q https://raw.githubusercontent.com/klarman-cell-observatory/cumulus/master/docker/monitor_script.sh -O /usr/local/src/ctat-mutations/WDL/monitor_script.sh
#RUN chmod a+rx /usr/local/src/ctat-mutations/WDL/monitor_script.sh
## STAR
WORKDIR $SRC
ENV STAR_VERSION=2.7.8a
RUN STAR_URL="https://github.com/alexdobin/STAR/archive/${STAR_VERSION}.tar.gz" &&\
wget -q -P $SRC $STAR_URL &&\
tar -xvf $SRC/${STAR_VERSION}.tar.gz -C $SRC && \
mv $SRC/STAR-${STAR_VERSION}/bin/Linux_x86_64_static/STAR /usr/local/bin && \
rm ${STAR_VERSION}.tar.gz
#~~~~~~~~~~~
## Picard tools
#~~~~~~~~~~~
WORKDIR $SRC
RUN wget https://github.com/broadinstitute/picard/releases/download/2.25.2/picard.jar
ENV PICARD_HOME $SRC/picard.jar
## Minimap2
WORKDIR $SRC
RUN curl -L https://github.com/lh3/minimap2/releases/download/v2.26/minimap2-2.26_x64-linux.tar.bz2 | tar -jxvf - && \
mv ./minimap2-2.26_x64-linux/minimap2 $BIN/
## NCIP CTAT mutations
RUN apt-get update && apt-get install -y git
WORKDIR $SRC
ENV CTAT_MUTATIONS_TAG=v4.0.0
ENV CTAT_MUTATIONS_COMMIT=e7f7b48f88a89fcda20e41ecb38916980ac096f2
RUN git clone https://github.com/NCIP/ctat-mutations.git && \
cd ctat-mutations && \
git checkout $CTAT_MUTATIONS_COMMIT && \
git submodule init && git submodule update && \
git submodule foreach --recursive git submodule init && \
git submodule foreach --recursive git submodule update && \
make
ENV PATH=/usr/local/src/gatk-${GATK_VERSION}:/usr/local/src/ctat-mutations/WDL/:$PATH
RUN apt-get -qq -y remove automake build-essential curl gcc g++ git make unzip wget && \
apt-get -qq -y autoremove && \
apt-get clean && \
rm -rf /var/lib/apt/lists/* /var/log/dpkg.log