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October 10, 2017, Tuesday

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Liya Wang edited this page Oct 14, 2017 · 6 revisions

  • For the main version (running on CSHL)

    • We will use this for publication and re-analysis with data hosted at CSHL
    • We will use this for workshop
    • Add checking for data size pulled from CyVerse
      • For file bigger than 1.9 GB, display 'File size is over the limit (1.9 GB), please use the community version of SciApps: de.sciapps.org'
      • How about folder size?

  • Conversion of apps from main version to community version

    • Build workflow from the main version
    • Log into the community version as 'maizecode'
    • Test the workflow after manually changing following components of the workflow json
      • Remove all job ids from the workflow json
      • Convert input path from sciapps.org to CyVerse community folder path
      • Create a copy of stampdede app for each cshl app
        • Change execution system from sciapps to stampede, and queue from debug to general
        • Gzip singularity images in a bin folder (can be more than one images)
        • Modify wrapper script to gunzip and run on TACC
        • Share with maizecode
      • Build the workflow?
    • Make public (or share the workflow with users logged into SciApps?)
      • Make all apps public
      • Re-run all analysis to create new workflow json (or ask user to use DE instead?)
      • Make all jobs and results public

  • Alternatively we can convert with following steps

    • Ship all inputs and results from CSHL to CyVerse
    • Modify workflow json to adopt the path changes, and app id change (from private to public one)
    • Make inputs and results public with Agave (can we use data commons link)
    • Load modified workflow json on the community version
      • History and workflow diagram can all point to the CyVerse copy of inputs and results
      • App forms will be loaded with the public version of apps
      • Re-run analysis will load the public app with associated inputs (assuming public app and private app are consistent on interface)
    • Drawback: do we still need to test whether individual public app is working or not?

  • Shift efforts back to the community version

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