September 11, 2018, Tuesday

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Liya Wang edited this page Sep 12, 2018 · 6 revisions

'Larger' files not uncompressed correctly
- Though it works on brie but not on halcott
- Reason is that the system tries to uncompress before Agave transferred it
- Solutions
  - Check file history to see whether 'staging_completed'
    - Need to add code to agavedancer/lib/Agave/Client/IO.pm
  - Add notification service, need more synchronization
  - Switch to icommands then uncompress (better solution)
Other issues
- Add jobs output link to details
  - Critical for debugging when a job fails
- Think about how to pull inputs with icommands with specified resource server?
- Submitted time changes when job status changes to running?
- Need to make job name shorter in History panel (messy when more than 20 jobs present. Since 2 takes more spaces than 1)
- Remove 'private' app, which is 'remote' in production.xml
Improvement
- Add 'normal' queue to our cluster to make it easy to switch
- Pre-stage genome index, build genome services for several genomes on TACC and CSHL
- Rewrite docs
  - Updated to step 4
  - Need to modify the Association workflow, especially the visualization part
  - Need to modify the Annotation tutorial, especially the visualization part
  - Need to create new workflows, especially the association part