Story #8002

Updated by Brett Smith over 4 years ago

I suggest we stop building it and revoke the previously-published packages. Nothing declares it as a dependency:

<pre>(arv)locke % git grep -i pyvcf .
docker/compute/Dockerfile:RUN apt-get install -qy supervisor python-pip python-pyvcf python-gflags python-google-api-python-client python-virtualenv libattr1-dev libfuse-dev python-dev python-llfuse crunchstat python-arvados-fuse cron dnsmasq
docker/shell/Dockerfile: python-pip python-pyvcf python-gflags python-google-api-python-client \
</pre>

(We'll need to remove these installs first.) And no Python code imports the module:

<pre>(arv)locke % find -name setup.py -print0 | xargs -0 dirname | xargs git grep -l vcf crunch_scripts
crunch_scripts/GATK2-VariantFiltration
crunch_scripts/GATK2-bqsr
crunch_scripts/GATK2-merge-call
crunch_scripts/GATK2-realign
sdk/python/tests/data/1000G_ref_manifest
sdk/python/tests/data/jlake_manifest
</pre>

The results are too much to paste here but the Crunch scripts all have the string 'vcf' in filenames, not from any module import. The Dockerfile suggests we were previously installing this on compute+shell nodes as a convenience for bioinformatics work, but the way we use Docker makes that moot now.

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