Story #8002

[Deployment] python-pyvcf backport is unnecessary

Added by Brett Smith over 3 years ago. Updated over 3 years ago.

Status:
Resolved
Priority:
Normal
Assigned To:
Brett Smith
Category:
Deployment
Target version:
Start date:
03/18/2016
Due date:
% Done:

100%

Estimated time:
(Total: 0.00 h)
Story points:
0.5

Description

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

(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 \

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

(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

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.


Subtasks

Task #8759: Review 8002-no-pyvcf-wipResolvedBrett Smith

Associated revisions

Revision 1c2af193
Added by Brett Smith over 3 years ago

Merge branch '8002-no-pyvcf-wip'

Closes #8002, #8759.

History

#1 Updated by Brett Smith over 3 years ago

  • Description updated (diff)

#2 Updated by Brett Smith over 3 years ago

Ward and Peter agree with my assessment on IRC.

#3 Updated by Brett Smith over 3 years ago

  • Category set to Deployment
  • Status changed from New to In Progress
  • Assigned To set to Brett Smith
  • Target version set to 2016-03-30 sprint
  • Story points set to 0.5

Bumping in priority because PyVCF has apparently made a broken release that is breaking our builds. e.g., https://ci.curoverse.com/job/build-packages/1791/

#4 Updated by Tom Clegg over 3 years ago

8002-no-pyvcf-wip @ cf82d85 LGTM, thanks.

If we had used this in arvados/jobs we could worry that someone's pipeline was still relying on it... but apparently, fortunately, we didn't.

#5 Updated by Brett Smith over 3 years ago

  • Status changed from In Progress to Resolved
  • % Done changed from 0 to 100

Applied in changeset arvados|commit:1c2af19398b425fb249e6fa8cc909500ce1fa80f.

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