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install conda packages to separate environment within Docker container #980

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merged 2 commits into from
Jul 31, 2019
Merged

install conda packages to separate environment within Docker container #980

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00ab6eb
resolve merge conflict
tomkinsc Jul 12, 2019
44c73b1
Merge branch 'master' into ct-install-conda-pkgs-to-separate-env-in-D…
tomkinsc Jul 17, 2019
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11 changes: 7 additions & 4 deletions Dockerfile
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Original file line number Diff line number Diff line change
Expand Up @@ -20,17 +20,20 @@ LABEL maintainer "viral-ngs@broadinstitute.org"
ENV \
INSTALL_PATH="/opt/viral-ngs" \
VIRAL_NGS_PATH="/opt/viral-ngs/source" \
MINICONDA_PATH="/opt/miniconda"
MINICONDA_PATH="/opt/miniconda" \
CONDA_DEFAULT_ENV=viral-ngs-env
ENV \
PATH="$VIRAL_NGS_PATH:$MINICONDA_PATH/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin" \
CONDA_DEFAULT_ENV=$MINICONDA_PATH \
CONDA_PREFIX=$MINICONDA_PATH \
PATH="$VIRAL_NGS_PATH:$MINICONDA_PATH/envs/$CONDA_DEFAULT_ENV/bin:$MINICONDA_PATH/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin" \
CONDA_PREFIX=$MINICONDA_PATH/envs/$CONDA_DEFAULT_ENV \
JAVA_HOME=$MINICONDA_PATH

# Prepare viral-ngs user and installation directory
# Set it up so that this slow & heavy build layer is cached
# unless the requirements* files or the install scripts actually change
WORKDIR $INSTALL_PATH
RUN conda create -n $CONDA_DEFAULT_ENV python=3.6
RUN echo "source activate $CONDA_DEFAULT_ENV" > ~/.bashrc
RUN hash -r
COPY docker/install-viral-ngs.sh $VIRAL_NGS_PATH/docker/
COPY requirements-minimal.txt $VIRAL_NGS_PATH/
RUN $VIRAL_NGS_PATH/docker/install-viral-ngs.sh minimal
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20 changes: 10 additions & 10 deletions docker/install-viral-ngs.sh
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Expand Up @@ -15,16 +15,14 @@

set -e -o pipefail

echo "PATH: ${PATH}"
echo "INSTALL_PATH: ${INSTALL_PATH}"
echo "CONDA_PREFIX: ${CONDA_PREFIX}"
echo "VIRAL_NGS_PATH: ${VIRAL_NGS_PATH}"
echo "MINICONDA_PATH: ${MINICONDA_PATH}"
echo "CONDA_DEFAULT_ENV: ${CONDA_DEFAULT_ENV}"
CONDA_CHANNEL_STRING="--override-channels -c broad-viral -c conda-forge -c bioconda -c defaults"

mkdir -p $INSTALL_PATH/viral-ngs-etc
if [ ! -f $INSTALL_PATH/viral-ngs-etc/viral-ngs ]; then
ln -s $VIRAL_NGS_PATH $INSTALL_PATH/viral-ngs-etc/viral-ngs
fi
if [ ! -f $INSTALL_PATH/viral-ngs-etc/conda-env ]; then
ln -s $CONDA_DEFAULT_ENV $INSTALL_PATH/viral-ngs-etc/conda-env
fi

# setup/install viral-ngs directory tree and conda dependencies
sync

Expand All @@ -33,13 +31,15 @@ if [[ "$1" == "minimal" ]]; then
# a more minimal set of tools (smaller docker image?)
conda install -y \
-q $CONDA_CHANNEL_STRING \
--file "$VIRAL_NGS_PATH/requirements-minimal.txt"
--file "$VIRAL_NGS_PATH/requirements-minimal.txt" \
-p "${CONDA_PREFIX}"
else
conda install -y \
-q $CONDA_CHANNEL_STRING \
--file "$VIRAL_NGS_PATH/requirements-py3.txt" \
--file "$VIRAL_NGS_PATH/requirements-conda.txt" \
--file "$VIRAL_NGS_PATH/requirements-conda-tests.txt"
--file "$VIRAL_NGS_PATH/requirements-conda-tests.txt" \
-p "${CONDA_PREFIX}"
fi

# clean up
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