User

Stephanie Gogarten

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Posts

Votes on activity by Stephanie Gogarten

  • Allow workflow input from multiple data tables

    It would be very helpful if a workflow could take inputs from multiple data tables. Not all use cases are covered by the <x>, <x>_set model as the only table combinations in a single workflow, for ...

    • 2 followers
    • 1 comment
    • 7 votes

  • Remove a workspace from "My Workspaces"?

    Is it possible to remove myself from a workspace that has been shared with me, so it no longer shows up in "My Workspaces"? It's frustrating to have my list of workspaces cluttered with relics of p...

    • 3 followers
    • 4 comments
    • 1 vote

  • Version control for notebooks

    How do other Terra users manage version control for notebooks?

    • 2 followers
    • 4 comments
    • 1 vote

  • Workflow outputs not displayed in Job History "outputs" tab

    In the main Job History page on Terra, the "Outputs" tab only contains values if the workflow was run on a data table. If the workflow was run on file paths so that outputs are not written to a dat...

    • Edited
    • 2 followers
    • 1 comment
    • 0 votes

  • Copy RStudio html output to notebooks/

    When syncing an RStudio notebook to the notebooks/ folder, it would be very helpful to copy the .nb.html file as well as the .Rmd file. This way users would be able to view the output of their note...

    • 2 followers
    • 1 comment
    • 0 votes

  • tnu drs commands returning error code

    I'm trying to use a controlled-access file with a drs link in the terminal from an RStudio cloud environment on Terra. I can copy the curl command to download the file via the File browser and run ...

    • 2 followers
    • 2 comments
    • 0 votes

  • Workflow succeeded despite error code

    I am writing a workflow that contains a series of commands in the command block. If the final command returns an error code, the workflow fails, but if an earlier command in the series returns an e...

    • Edited
    • 2 followers
    • 1 comment
    • 0 votes

  • Size limits on data tables?

    We are trying to create very large data tables in a workspace to track simulated genotype data. We are using the Bioconductor::AnVIL R functions avtable_import and avtable_import_set to write to th...

    • 2 followers
    • 1 comment
    • 0 votes

  • Latest 1000G VCF files on AnVIL?

    Are the most recent VCF files from the high-coverage 1000 Genomes dataset available on AnVIL, or are there plans to make them available soon? The 1000 Genomes public workspace only has the much old...

    • 2 followers
    • 1 comment
    • 0 votes

  • Error "Permission 'storage.buckets.list' denied on resource" when using gsutil

    Following the instructions in the support articles here and here leads to errors with `gsutil ls`: stephanie Applications $ ./google-cloud-sdk/bin/gsutil lsAccessDeniedException: 403 sdmorris@uw.ed...

    • Edited
    • 2 followers
    • 9 comments
    • 0 votes