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Story #8176

closed

[Crunch] cwl-runner needs to be refreshed

Added by Brett Smith about 9 years ago. Updated almost 9 years ago.

Status:
Resolved
Priority:
Normal
Assigned To:
Peter Amstutz
Category:
-
Target version:
2016-02-17 Sprint
Start date:
01/11/2016
Due date:
% Done:

100%

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

Description

Run a bcbio CWL pipeline and determine what if anything needs to be fixed.

Files

test_bcbio_cwl.tar.gz (14 MB) test_bcbio_cwl.tar.gz Peter Amstutz, 02/16/2016 09:30 PM

Subtasks 1 (0 open — 1 closed)

Task #8350: Review 8319-bcbio-cwlResolvedSarah Guthrie01/11/2016

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 #1

Updated by Brett Smith about 9 years ago

  • Subject changed from [Crunch] `cwl runner` needs to be refreshed to [Crunch] cwl-runner needs to be refreshed
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 #2

Updated by Brett Smith about 9 years ago

  • Target version set to 2016-02-03 Sprint
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 #3

Updated by Brett Smith about 9 years ago

  • Target version changed from 2016-02-03 Sprint to 2016-02-17 Sprint

Plan is to scope this during the 3 Feb sprint and then fix during 17 Feb sprint at latest.

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 #4

Updated by Peter Amstutz almost 9 years ago

  • Story points set to 0.5
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 #5

Updated by Peter Amstutz almost 9 years ago

  • Description updated (diff)

Branch 8319-bcbio-cwl with the following improvements:

  • Fix resolving files referenced in an arv-mount directory to correct keep references
  • Handle null output field of failed jobs
  • cwltool fixes improving naming of individual jobs. Update cwltool pin.
  • New feature, create a pipeline_instance and dynamically add components to the pipeline instance so that the job can be viewed from workbench.
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 #6

Updated by Peter Amstutz almost 9 years ago

  • Assigned To set to Peter Amstutz
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 #7

Updated by Brett Smith almost 9 years ago

  • Status changed from New to In Progress
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 #9

Updated by Peter Amstutz almost 9 years ago

  1. checkout arvados branch 8319-bcbio-cwl
  2. setup a virtualenv environment
  3. cd arvados/sdk/python && python setup.py install
  4. cd arvados/sdk/cwl && python setup.py install
  5. Download & untar test_bcbio_cwl.tar.gz
  6. cd test_bcbio_cwl
  7. arv-put --portable-data-hash --name "bcbio testdata" testdata
  8. mv testdata orig-testdata
  9. arv-mount --collection 13feeb0c70e6f1e3ab7d4787549435a1+2411 testdata
  10. cwl-runner run_info-cwl-workflow/main-run_info-cwl.cwl run_info-cwl-workflow/main-run_info-cwl-samples.json
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 #10

Updated by Sarah Guthrie almost 9 years ago

Ready to merge - it runs and looks good to me

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 #11

Updated by Peter Amstutz almost 9 years ago

  • Status changed from In Progress to Resolved

Handled in #8319

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