anchor.diff:  RUN cd /ensembl-vep-release-${VEP_VERSION} && perl INSTALL.pl -a ap -n -l -g all
   RUN ln -s /ensembl-vep-release-${VEP_VERSION}/vep /vep
   
  +# clone and hail-elasticsearch-pipelines repo
  +RUN git clone https://github.com/macarthur-lab/hail-elasticsearch-pipelines.git
  +RUN cd hail-elasticsearch-pipelines && git checkout fix_hail_common_dependencies
  +RUN python3 -m pip install -r /hail-elasticsearch-pipelines/luigi_pipeline/requirements.txt
  +
   COPY vep-GRCh37.json /
   COPY vep-GRCh38.json /
   
  
positive.code: 	&& make install \
  	&& make clean
  
  # install gcloud tools
  RUN python3 -m pip install --upgrade pip
  
  
negative.code: RUN /google-cloud-sdk/install.sh -q
  
  # python packages
  RUN python3 -m pip install --upgrade gsutil
  
  # install GCS connector using the same steps as in https://raw.githubusercontent.com/broadinstitute/install-gcs-connector/master/install_gcs_connector.py
  # assumes ~/.config/gcloud/application_default_credentials.json will be mounted into the docker container
  RUN python3 -m pip install hail
  COPY spark-defaults.conf /usr/local/lib/python3.7/site-packages/pyspark/conf/spark-defaults.conf
  RUN wget https://repo1.maven.org/maven2/com/google/cloud/bigdataoss/gcs-connector/hadoop2-1.9.17/gcs-connector-hadoop2-1.9.17-shaded.jar -O /usr/local/lib/python3.7/site-packages/pyspark/jars/gcs-connector-hadoop2-1.9.17-shaded.jar
  
  