<commit_before>FROM stackbrew/ubuntu:14.04
MAINTAINER <NAME> "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/chapmanb/bcbio-nextgen/master/scripts/bcbio_nextgen_install.py && \
    python bcbio_nextgen_install.py /usr/local/share/bcbio-nextgen \
      --isolate --nodata -u development --tooldir=/usr/local && \
    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 mysql && \
    /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 && \<commit_msg>Docker: mysql-connector-c for UCSC tools<commit_after>FROM stackbrew/ubuntu:14.04
MAINTAINER <NAME> "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/chapmanb/bcbio-nextgen/master/scripts/bcbio_nextgen_install.py && \
    python bcbio_nextgen_install.py /usr/local/share/bcbio-nextgen \
      --isolate --nodata -u development --tooldir=/usr/local && \
    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 mysql && \
    /usr/local/share/bcbio-nextgen/anaconda/bin/conda remove --force -y mysql-connector-c && \
    /usr/local/share/bcbio-nextgen/anaconda/bin/conda install -y -c conda-forge -c bioconda mysql-connector-c && \
    /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 && \
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