anchor.diff:  COPY bashrc_custom /root/.bashrc_custom
   COPY entrypoint.sh /
   
  +COPY core-site.xml /usr/local/spark-2.0.2-bin-hadoop2.7/conf/
  +
  +
   WORKDIR /seqr
   
   CMD [ "/entrypoint.sh" ]
  
positive.code:     && mv ./kubectl /usr/local/bin/kubectl
  
  # install picard
  RUN mkdir /picard \
      && cd /picard \
      && wget https://github.com/broadinstitute/picard/releases/download/2.15.0/picard.jar
  
  # download LiftoverChain files
  RUN mkdir -p /reference-data \
      && cd /reference-data \
      && wget http://hgdownload.cse.ucsc.edu/goldenPath/hg38/bigZips/hg38.fa.gz \
      && wget http://hgdownload.cse.ucsc.edu/goldenPath/hg19/liftOver/hg19ToHg38.over.chain.gz
  
  # install VEP - steps taken from gs://hail-common/vep/vep/GRCh38/vep85-GRCh38-init.sh
  RUN mkdir -p /vep/homo_sapiens \
      && gsutil -m cp -r gs://hail-common/vep/vep/loftee /vep  \
      && gsutil -m cp -r gs://hail-common/vep/vep/ensembl-tools-release-85 /vep  \
      && gsutil -m cp -r gs://hail-common/vep/vep/GRCh38/loftee_data /vep  \
      && gsutil -m cp -r gs://hail-common/vep/vep/Plugins /vep  \
      && gsutil -m cp -r gs://hail-common/vep/vep/homo_sapiens/85_GRCh38 /vep/homo_sapiens/
  
  RUN gsutil cp gs://hail-common/vep/vep/GRCh38/vep85-GRCh38-gcloud.properties /vep/vep-gcloud.properties \
      && gsutil cp gs://hail-common/vep/htslib/* /usr/bin/ \
      && gsutil cp gs://hail-common/vep/samtools /usr/bin/ \
      && chmod a+rx  /usr/bin/tabix /usr/bin/bgzip /usr/bin/htsfile /usr/bin/samtools
  
  RUN ln -s /vep/ensembl-tools-release-85/scripts/variant_effect_predictor /vep/variant_effect_predictor \
      && gsutil cp gs://hail-common/vep/vep/GRCh38/run_hail_vep85_GRCh38_vcf.sh /vep/run_hail_vep85_vcf.sh  \
      && chmod a+rx /vep/run_hail_vep85_vcf.sh
  
  RUN wget https://raw.github.com/miyagawa/cpanminus/master/cpanm -O /usr/bin/cpanm \
      && chmod +x /usr/bin/cpanm \
      && cpanm --notest CGI DBI JSON
  
  # run VEP on the 1-variant VCF to create fasta.index file -- caution do not make fasta.index file writeable afterwards!
  RUN gsutil cp gs://hail-common/vep/vep/1var.vcf /vep  \
      && /vep/run_hail_vep85_vcf.sh /vep/1var.vcf
  
  # install hail
  RUN cd /usr/local \
      && wget -nv http://apache.cs.utah.edu/spark/spark-2.0.2/spark-2.0.2-bin-hadoop2.7.tgz \
      && tar xzf /usr/local/spark-2.0.2-bin-hadoop2.7.tgz
  
  RUN cd / \
      && git clone --branch 0.1 https://github.com/broadinstitute/hail.git \
      && cd /hail \
      && ./gradlew -Dspark.version=2.0.2 shadowJar
  
  #RUN cd /hail \
  #    && ./gradlew -Dspark.version=2.0.2 installDist \
  #    && rm ./build/install/hail/lib/asm-3.1.jar
  
  WORKDIR /seqr
  
  
negative.code:     && pip install --upgrade -r requirements.txt
  
  COPY shared/config/*.py /seqr_settings/
  
  
  ENV PYTHONPATH="$PYTHONPATH:/seqr:/seqr_settings"
  