Merge 44c73b1 into b85cdd3

Dockerfile

@@ -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

docker/install-viral-ngs.sh

@@ -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
 
@@ -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