Bug #11621

Example CWL code for cwl-runner doesn't work

Added by Sarah Zaranek over 2 years ago. Updated 6 months ago.

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when I run
arvados-cwl-runner bwa-mem.cwl bwa-mem-input.yml

I get the following:
017-05-04 18:38:57 cwltool INFO: /usr/bin/arvados-cwl-runner b04638275cff9b393e1bc04136d44f361b999cf8 1.0.20170420181844, arvados-python-client 0.1.20170420181844, cwltool 1.0.20170413194156
2017-05-04 18:38:57 cwltool INFO: Resolved 'bwa-mem.cwl' to 'file:///home/sarah/cwl/arvados/doc/user/cwl/bwa-mem/bwa-mem.cwl'
2017-05-04 18:38:58 cwltool INFO: ['docker', 'pull', 'biodckr/bwa']
Using default tag: latest
Pulling repository docker.io/biodckr/bwa
Error: image biodckr/bwa:latest not found
2017-05-04 18:38:59 cwltool ERROR: Workflow error, try again with --debug for more information:
bwa-mem.cwl:7:5: Command '['docker', 'pull', 'biodckr/bwa']' returned non-zero exit status 1

Talked to Peter. Said that docker image might not exist anymore. Should probably update the code with a new docker image.

Associated revisions

Revision b3efaa37
Added by Tom Clegg over 1 year ago

Merge branch 'patch-2' of https://github.com/jrandall/arvados

fixes #11621

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <>


#1 Updated by Tom Morris almost 2 years ago

  • Target version set to Arvados Future Sprints

#2 Updated by Joshua Randall over 1 year ago

  • Category set to Documentation

I just went to report this as well and found it was already reported. bwa-mem cwl example does not work as the `biodckr/bwa` docker repo no longer exists.

#3 Updated by Joshua Randall over 1 year ago

  • % Done changed from 0 to 100

#4 Updated by Anonymous over 1 year ago

  • Status changed from New to Resolved

#5 Updated by Tom Morris 6 months ago

  • Target version deleted (Arvados Future Sprints)

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