Need Help?

Search our documentation and community forum

Terra is a cloud-native platform for biomedical researchers to access data, run analysis tools, and collaborate.
Terra powers important scientific projects like FireCloud, AnVIL, and BioData Catalyst. Learn more.

Detachable Persistent Disks




  • Avatar
    Nicole Deflaux

    Sometimes `pip install --upgrade <pkg>` does not work successfully and people need to troubleshoot.

    Now that package installs are written to the Terra detachable persistent disk, one approach is to delete and recreate that disk to troubleshoot BUT it's easy to forget that you have some important files on that disk, then delete it during a troubleshooting session and regret the deletion.

    An alternative is to troubleshoot by starting from an empty `packages/` directory. For example, open a terminal and then run the following commands to move all currently installed packages to another directory so that they are no longer visible to pip, Python, and Jupyter:

    cd $HOME/notebooks

    export PKG_STASH_DIR=packages-as-of-$(date +"%Y%m%d")

    mkdir $PKG_STASH_DIR

    # Move all the currently installed packages out of the existing destination directory for package installations.
    mv packages/* $PKG_STASH_DIR

    Now you can retry the `pip`  commands to install the packages again!

    Comment actions Permalink
  • Avatar
    Tiffany Miller

    Note that Rstudio rmd files are not auto-syncing to the Google bucket. This feature should be released by the end of 2021.

    Comment actions Permalink

Please sign in to leave a comment.

Powered by Zendesk