Reverting virtualenv implementation due to CNVnator bug

Dockerfile

@@ -14,11 +14,16 @@ ENV DYLD_LIBRARY_PATH=/usr/lib/root/lib
 ENV HTSLIB_LIBRARY_DIR=/usr/local/lib
 ENV HTSLIB_INCLUDE_DIR=/usr/local/include
 
-WORKDIR /
-
 # System packages 
 RUN apt-get update && apt-get install -y curl wget
 
+# Install miniconda to /miniconda
+RUN curl -LO http://repo.continuum.io/miniconda/Miniconda-latest-Linux-x86_64.sh
+RUN bash Miniconda-latest-Linux-x86_64.sh -p /miniconda -b
+RUN rm Miniconda-latest-Linux-x86_64.sh
+ENV PATH=/miniconda/bin:${PATH}
+RUN conda update -y conda
+
 RUN /bin/bash -c "echo 'deb http://dnanexus-apt-prod.s3.amazonaws.com/ubuntu trusty/amd64/' > /etc/apt/sources.list.d/dnanexus.list"
 RUN /bin/bash -c "echo 'deb http://dnanexus-apt-prod.s3.amazonaws.com/ubuntu trusty/all/' >> /etc/apt/sources.list.d/dnanexus.list"
 RUN wget https://wiki.dnanexus.com/images/files/ubuntu-signing-key.gpg
@@ -68,25 +73,6 @@ RUN apt-get update -y && apt-get upgrade -y && apt-get install -y --force-yes \
     zlib1g-dev
 RUN apt-get update
 
-# Install virtualenv
-RUN pip install --upgrade pip 
-RUN pip install virtualenv
-
-# Create BreakSeq virtualenv
-RUN virtualenv breakseq2
-RUN /bin/bash -c "source /breakseq2/bin/activate && apt-get install -y --force-yes python-dev && pip install https://github.com/bioinform/breakseq2/archive/2.2.tar.gz && deactivate"
-
-# Create svviz virtualenv
-RUN virtualenv svviz
-RUN /bin/bash -c "source /svviz/bin/activate && pip install svviz && deactivate"
-
-# Install miniconda to /miniconda
-RUN curl -LO http://repo.continuum.io/miniconda/Miniconda-latest-Linux-x86_64.sh
-RUN bash Miniconda-latest-Linux-x86_64.sh -p /miniconda -b
-RUN rm Miniconda-latest-Linux-x86_64.sh
-ENV PATH=/miniconda/bin:${PATH}
-RUN conda update -y conda
-
 RUN conda config --add channels r
 RUN conda config --add channels conda-forge
 RUN conda config --add channels bioconda
@@ -97,13 +83,16 @@ RUN conda install -c bioconda samblaster -y
 RUN conda install -y -c anaconda networkx
 RUN conda install gcc_linux-64 -y
 RUN conda install -c bioconda manta
-RUN conda install -y numpy
 
 WORKDIR /
 ADD resources.tar.gz /
 RUN cp -a /resources/* /
 RUN rm -rf /resources/
 
+RUN conda install -y numpy
+RUN pip install --upgrade pip 
+RUN pip install https://github.com/bioinform/breakseq2/archive/2.2.tar.gz
+
 RUN pip install dxpy
 
 WORKDIR /root

dx_app_code/parliament2/dxapp.json

@@ -254,5 +254,5 @@
       }
     }
   },
-  "openSource": true
+  "openSource": false
 }

parliament2.sh

@@ -74,7 +74,6 @@ fi
 # BREAKSEQ2
 if [[ "$run_breakseq" == "True" ]]; then
     echo "BreakSeq"
-    source "/breakseq2/bin/activate"
     bplib="/breakseq2_bplib_20150129/breakseq2_bplib_20150129.gff"
     work="breakseq2"
     timeout 6h ./breakseq2-2.2/scripts/run_breakseq2.py --reference ref.fa \
@@ -286,6 +285,11 @@ wait
 # Run SVtyper and SVviz
 if [[ "$run_genotype_candidates" == "True" ]]; then
     echo "Running SVTyper"
+    # SVviz and BreakSeq have mutually exclusive versions of pysam required, so
+    # SVviz is only installed later and if necessary
+    if [[ "$run_svviz" == "True" ]]; then
+        pip install svviz -q &
+    fi
 
     mkdir -p /home/dnanexus/out/svtyped_vcfs/
     set -e
@@ -389,7 +393,6 @@ if [[ "$run_genotype_candidates" == "True" ]]; then
     # Run svviz
     if [[ "$run_svviz" == "True" ]]; then
         echo "Running svviz"
-        source "/svviz/bin/activate"
         mkdir svviz_outputs
 
         grep \# survivor_sorted.vcf > header.txt