anchor.diff:  # DISABLE_CACHE work-around to force git pull on every docker build, based on https://github.com/docker/docker/issues/1996
   ARG DISABLE_CACHE=1
   
  -# install hail-elasticsearch-pipelines
  +# clone hail-elasticsearch-pipelines
   RUN git clone https://github.com/macarthur-lab/hail-elasticsearch-pipelines.git /hail-elasticsearch-pipelines
  +
  +# copy loftee
   RUN cp -r /hail-elasticsearch-pipelines/loftee /vep \
       && cp /hail-elasticsearch-pipelines/gcloud_dataproc/vep_init/vep-gcloud-grch38.properties /vep/vep-gcloud-grch38.properties \
       && cp /hail-elasticsearch-pipelines/gcloud_dataproc/vep_init/vep-gcloud-grch37.properties /vep/vep-gcloud-grch37.properties \
  
positive.code: 
  RUN wget https://storage.googleapis.com/hadoop-lib/gcs/gcs-connector-latest-hadoop2.jar -O /usr/local/spark-2.0.2-bin-hadoop2.7/jars/gcs-connector-latest-hadoop2.jar
  
  # install hail
  RUN mkdir -p /hail/build/libs /hail/build/distributions \
      && gsutil cp gs://seqr-hail/hail-jar/hail-0.1-es-6.2.4-with-strip-chr-prefix.zip /hail/build/distributions/hail-python.zip \
      && gsutil cp gs://seqr-hail/hail-jar/hail-0.1-es-6.2.4-with-strip-chr-prefix.jar /hail/build/libs/hail-all-spark.jar
  
  # install jupyter
  RUN pip install --upgrade pip jupyter
  
  
negative.code:     && cp /hail-elasticsearch-pipelines/gcloud_dataproc/vep_init/run_hail_vep85_GRCh38_vcf.sh /vep/run_hail_vep85_GRCh38_vcf.sh \
      && cp /hail-elasticsearch-pipelines/gcloud_dataproc/vep_init/1var.vcf /vep/1var.vcf
  
  # copy hail build
  RUN mkdir -p /hail/build/libs /hail/build/distributions \
      && cp /hail-elasticsearch-pipelines/hail_builds/v01/hail-9-17-2018-f3e47061.zip /hail/build/distributions/hail-python.zip \
      && cp /hail-elasticsearch-pipelines/hail_builds/v01/hail-9-17-2018-f3e47061.jar /hail/build/libs/hail-all-spark.jar
  
  
  # run VEP on the 1-variant VCF to create fasta.index file
  RUN /vep/run_hail_vep85_GRCh37_vcf.sh /vep/1var.vcf \
  