Story #8176
closed
[Crunch] cwl-runner needs to be refreshed
Added by Brett Smith about 9 years ago.
Updated almost 9 years ago.
Estimated time:
(Total: 0.00 h)
Description
Run a bcbio CWL pipeline and determine what if anything needs to be fixed.
Files
- Subject changed from [Crunch] `cwl runner` needs to be refreshed to [Crunch] cwl-runner needs to be refreshed
- Target version set to 2016-02-03 Sprint
- 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.
- 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.
- Assigned To set to Peter Amstutz
- Status changed from New to In Progress
- checkout arvados branch 8319-bcbio-cwl
- setup a virtualenv environment
- cd arvados/sdk/python && python setup.py install
- cd arvados/sdk/cwl && python setup.py install
- Download & untar test_bcbio_cwl.tar.gz
- cd test_bcbio_cwl
- arv-put --portable-data-hash --name "bcbio testdata" testdata
- mv testdata orig-testdata
- arv-mount --collection 13feeb0c70e6f1e3ab7d4787549435a1+2411 testdata
- cwl-runner run_info-cwl-workflow/main-run_info-cwl.cwl run_info-cwl-workflow/main-run_info-cwl-samples.json
Ready to merge - it runs and looks good to me
- Status changed from In Progress to Resolved
Also available in: Atom
PDF
Updated by 
Updated by 
Updated by Sarah Guthrie