Bug #11621: Example CWL code for cwl-runner doesn't work - Arvados

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Bug #11621

closed

Example CWL code for cwl-runner doesn't work

Added by Sarah Zaranek almost 7 years ago. Updated about 5 years ago.

Status:

Resolved

Priority:

Normal

Assigned To:

Category:

Documentation

Target version:

Story points:

Description

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.

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Updated by Tom Morris over 6 years ago

Target version set to Arvados Future Sprints

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Updated by Joshua Randall over 6 years 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.

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