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Merge pull request #69 from cancerit/feature/docker
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| /LICENCE | ||
| /prerelease.sh | ||
| /README.md | ||
| /INSTALL | ||
| /LICENCE | ||
| /CHANGES.md | ||
| /.gitignore | ||
| /.git | ||
| /perl/docs | ||
| /perl/docs.tar.gz |
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| FROM quay.io/wtsicgp/dockstore-cgpmap:3.1.4 as builder | ||
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| USER root | ||
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| # ALL tool versions used by opt-build.sh | ||
| ENV VER_CGPVCF="v2.2.1" | ||
| ENV VER_VCFTOOLS="0.1.16" | ||
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| RUN apt-get -yq update | ||
| RUN apt-get install -yq --no-install-recommends \ | ||
| locales \ | ||
| g++ \ | ||
| make \ | ||
| gcc \ | ||
| pkg-config \ | ||
| zlib1g-dev | ||
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| RUN locale-gen en_US.UTF-8 | ||
| RUN update-locale LANG=en_US.UTF-8 | ||
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| ENV OPT /opt/wtsi-cgp | ||
| ENV PATH $OPT/bin:$OPT/biobambam2/bin:$PATH | ||
| ENV PERL5LIB $OPT/lib/perl5 | ||
| ENV LD_LIBRARY_PATH $OPT/lib | ||
| ENV LC_ALL en_US.UTF-8 | ||
| ENV LANG en_US.UTF-8 | ||
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| # build tools from other repos | ||
| ADD build/opt-build.sh build/ | ||
| RUN bash build/opt-build.sh $OPT | ||
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| # build the tools in this repo, separate to reduce build time on errors | ||
| COPY . . | ||
| RUN bash build/opt-build-local.sh $OPT | ||
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| FROM ubuntu:16.04 | ||
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| LABEL maintainer="[email protected]" \ | ||
| uk.ac.sanger.cgp="Cancer, Ageing and Somatic Mutation, Wellcome Trust Sanger Institute" \ | ||
| version="1.0.0" \ | ||
| description="cgpPindel docker" | ||
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| RUN apt-get -yq update | ||
| RUN apt-get install -yq --no-install-recommends \ | ||
| apt-transport-https \ | ||
| locales \ | ||
| curl \ | ||
| ca-certificates \ | ||
| libperlio-gzip-perl \ | ||
| bzip2 \ | ||
| psmisc \ | ||
| time \ | ||
| zlib1g \ | ||
| liblzma5 \ | ||
| libncurses5 \ | ||
| p11-kit \ | ||
| unattended-upgrades && \ | ||
| unattended-upgrade -d -v && \ | ||
| apt-get remove -yq unattended-upgrades && \ | ||
| apt-get autoremove -yq | ||
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| RUN locale-gen en_US.UTF-8 | ||
| RUN update-locale LANG=en_US.UTF-8 | ||
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| ENV OPT /opt/wtsi-cgp | ||
| ENV PATH $OPT/bin:$OPT/biobambam2/bin:$PATH | ||
| ENV PERL5LIB $OPT/lib/perl5 | ||
| ENV LD_LIBRARY_PATH $OPT/lib | ||
| ENV LC_ALL en_US.UTF-8 | ||
| ENV LANG en_US.UTF-8 | ||
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| RUN mkdir -p $OPT | ||
| COPY --from=builder $OPT $OPT | ||
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| ## USER CONFIGURATION | ||
| RUN adduser --disabled-password --gecos '' ubuntu && chsh -s /bin/bash && mkdir -p /home/ubuntu | ||
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| USER ubuntu | ||
| WORKDIR /home/ubuntu | ||
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| CMD ["/bin/bash"] |
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| #! /bin/bash | ||
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| set -xe | ||
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| if [[ -z "${TMPDIR}" ]]; then | ||
| TMPDIR=/tmp | ||
| fi | ||
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| set -u | ||
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| if [ "$#" -lt "1" ] ; then | ||
| echo "Please provide an installation path such as /opt/ICGC" | ||
| exit 1 | ||
| fi | ||
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| # get path to this script | ||
| SCRIPT_PATH=`dirname $0`; | ||
| SCRIPT_PATH=`(cd $SCRIPT_PATH && pwd)` | ||
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| # get the location to install to | ||
| INST_PATH=$1 | ||
| mkdir -p $1 | ||
| INST_PATH=`(cd $1 && pwd)` | ||
| echo $INST_PATH | ||
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| # get current directory | ||
| INIT_DIR=`pwd` | ||
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| CPU=`grep -c ^processor /proc/cpuinfo` | ||
| if [ $? -eq 0 ]; then | ||
| if [ "$CPU" -gt "6" ]; then | ||
| CPU=6 | ||
| fi | ||
| else | ||
| CPU=1 | ||
| fi | ||
| echo "Max compilation CPUs set to $CPU" | ||
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| SETUP_DIR=$INIT_DIR/install_tmp | ||
| mkdir -p $SETUP_DIR/distro # don't delete the actual distro directory until the very end | ||
| mkdir -p $INST_PATH/bin | ||
| cd $SETUP_DIR | ||
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| # make sure tools installed can see the install loc of libraries | ||
| set +u | ||
| export LD_LIBRARY_PATH=`echo $INST_PATH/lib:$LD_LIBRARY_PATH | perl -pe 's/:\$//;'` | ||
| export PATH=`echo $INST_PATH/bin:$PATH | perl -pe 's/:\$//;'` | ||
| export MANPATH=`echo $INST_PATH/man:$INST_PATH/share/man:$MANPATH | perl -pe 's/:\$//;'` | ||
| export PERL5LIB=`echo $INST_PATH/lib/perl5:$PERL5LIB | perl -pe 's/:\$//;'` | ||
| set -u | ||
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| ## cgpPindel - should be the build root | ||
| if [ ! -e $SETUP_DIR/cgpPindel.success ]; then | ||
| cd $INIT_DIR | ||
| if [ ! -e $SETUP_DIR/cgpPindel_c.success ]; then | ||
| g++ -O3 -o $INST_PATH/bin/pindel c++/pindel.cpp | ||
| g++ -O3 -o $INST_PATH/bin/filter_pindel_reads c++/filter_pindel_reads.cpp | ||
| touch $SETUP_DIR/cgpPindel_c.success | ||
| fi | ||
| cd perl | ||
| cpanm --no-interactive --notest --mirror http://cpan.metacpan.org --notest -l $INST_PATH --installdeps . | ||
| cpanm -v --no-interactive --mirror http://cpan.metacpan.org -l $INST_PATH . | ||
| cd $SETUP_DIR | ||
| touch $SETUP_DIR/cgpPindel.success | ||
| fi |
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