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FROM stackbrew/ubuntu:14.04
MAINTAINER Brad Chapman "https://github.com/chapmanb"
# Setup a base system
RUN apt-get update && \
apt-get install -y curl wget git unzip tar gzip bzip2 xz-utils pigz && \
# Support inclusion in Arvados pipelines
apt-get install -y --no-install-recommends libcurl4-gnutls-dev mbuffer python2.7-dev python-virtualenv && \
# Not added by default to save space
# apt-get install -y libglu1-mesa && \
# bcbio-nextgen installation
mkdir -p /tmp/bcbio-nextgen-install && cd /tmp/bcbio-nextgen-install && \
wget --no-check-certificate \
https://raw.github.com/bcbio/bcbio-nextgen/master/scripts/bcbio_nextgen_install.py && \
python bcbio_nextgen_install.py /usr/local/share/bcbio-nextgen \
--isolate --minimize-disk --nodata -u development && \
git config --global url.https://github.com/.insteadOf git://github.com/ && \
/usr/local/share/bcbio-nextgen/anaconda/bin/conda install -y nomkl && \
/usr/local/share/bcbio-nextgen/anaconda/bin/bcbio_nextgen.py upgrade --isolate --tooldir=/usr/local --tools && \
/usr/local/share/bcbio-nextgen/anaconda/bin/bcbio_nextgen.py upgrade --isolate -u development --tools && \
# Remove larger packages not used consistently in bcbio Docker runs
/usr/local/share/bcbio-nextgen/anaconda/bin/conda remove --force -y hap.py && \
/usr/local/share/bcbio-nextgen/anaconda/bin/conda remove --force -y bioconductor-org.hs.eg.db bioconductor-org.mm.eg.db bioconductor-go.db && \
# setup paths
echo 'export PATH=/usr/local/bin:$PATH' >> /etc/profile.d/bcbio.sh && \
# add user run script
wget --no-check-certificate -O createsetuser \
https://raw.github.com/bcbio/bcbio-nextgen-vm/master/scripts/createsetuser && \
chmod a+x createsetuser && mv createsetuser /sbin && \
# clean filesystem
cd /usr/local && \
apt-get clean && \
rm -rf /var/lib/apt/lists/* /var/tmp/* && \
/usr/local/share/bcbio-nextgen/anaconda/bin/conda clean --yes --tarballs && \
# Remove large conda packages left behind
rm -rf /usr/local/share/bcbio-nextgen/anaconda/pkgs/qt* && \
rm -rf /usr/local/share/bcbio-nextgen/anaconda/pkgs/mysql-5.* && \
rm -rf /usr/local/share/bcbio-nextgen/anaconda/pkgs/hap.py.* && \
rm -rf /usr/local/share/bcbio-nextgen/anaconda/pkgs/scipy-0.19.1-np113py27_nomkl_0 && \
rm -rf /usr/local/share/bcbio-nextgen/anaconda/pkgs/bioconductor-org.*db* && \
rm -rf /usr/local/share/bcbio-nextgen/anaconda/pkgs/bioconductor-go.*db* && \
rm -rf /usr/local/share/bcbio-nextgen/anaconda/zulu*.tar.gz && \
rm -rf /usr/local/.git && \
rm -rf /.cpanm && \
rm -rf /tmp/bcbio-nextgen-install && \
# Create directories and symlinks for data
mkdir -p /mnt/biodata && \
mkdir -p /tmp/bcbio-nextgen && \
mv /usr/local/share/bcbio-nextgen/galaxy/bcbio_system.yaml /usr/local/share/bcbio-nextgen/config && \
rmdir /usr/local/share/bcbio-nextgen/galaxy && \
ln -s /mnt/biodata/galaxy /usr/local/share/bcbio-nextgen/galaxy && \
ln -s /mnt/biodata/gemini_data /usr/local/share/bcbio-nextgen/gemini_data && \
ln -s /mnt/biodata/genomes /usr/local/share/bcbio-nextgen/genomes && \
ln -s /mnt/biodata/liftOver /usr/local/share/bcbio-nextgen/liftOver && \
chmod a+rwx /usr/local/share/bcbio-nextgen && \
chmod a+rwx /usr/local/share/bcbio-nextgen/config && \
chmod a+rwx /usr/local/share/bcbio-nextgen/config/*.yaml && \
# Ensure permissions are set for update in place by arbitrary users
find /usr/local -perm /u+x -execdir chmod a+x {} \; && \
find /usr/local -perm /u+w -execdir chmod a+w {} \;