July 2018 Release Notes

Posted by KateN on 10 Jul 2018 (0)

July 31, 2018

  • FireCloud has upgraded to Cromwell 34. See release notes for versions 33 and 34 for new features available to you here.
    • WDL 1.0 support, requester pays, and PAPI v2 are not yet available in FireCloud. Work is underway to implement these specific components.
  • Notebooks clusters should no longer auto-pause when a Jupyter notebook or a terminal is open in a user's browser.
  • Leo now contains an optional user script that can be used to install GATK on clusters.
  • The notebooks docker image now includes the tidyverse R package by default.
  • Leo now contains an optional user script to allow downloading notebooks as PDF files. Note this significantly increases the size of the notebooks image which leads to slower cluster creation time, so use with caution. A follow-on change will be made to disallow downloading as PDF if this script is not used.
  • FireCloud no longer tracks user behaviors in Google Analytics.
  • Minor performance improvement via reducing unnecessary ajax requests when switching tabs inside a workspace.
  • Performance improvement via caching of WDL validation. Users may notice improved performance when viewing a method configuration inside a workspace.

July 24, 2018

  • You can now pause & resume clusters in the Notebooks tab. (previously this required an API call)
  • Jupyter bash terminal now supports history, tab completion, and colors.
  • FireCloud no longer requires the OAuth scope to "Manage your data and permissions in Google Cloud Storage" when logging in.
  • Selecting and copying gs:// and dos:// urls from within the FireCloud UI no longer copies extraneous unprintable/invisible characters.

July 17, 2018

  • You can now populate method config inputs directly from a JSON file.
  • Fixed an issue that caused timeouts and errors when attempting to view a workflow that contains many subworkflows.
  • Cluster creation now takes an optional value for the cluster auto-pause threshold. If not specified, a system default will be used. See Leonardo swagger for details on the new setting.

July 10, 2018

  • You can now install JupyterLab on Notebooks-created clusters. To do so, specify the following in the createCluster request:
    "userJupyterExtensionConfig": {
        "nbExtensions": {},
        "serverExtensions": {"jupyterlab": "jupyterlab"},
        "combinedExtensions": {}

    Once the cluster is created, JupyterLab can be accessed by appending /lab to the notebooks URL. For example: https://notebooks.firecloud.org/notebooks/project/cluster/lab.

  • Notebooks will now return a descriptive error message when trying to create a cluster in a project where Dataproc is not enabled.
  • Improved readability of the error message when adding a non-existent user to a group.
  • Fixed a bug that caused an individual workflow's details from displaying, in cases where the system encountered an unexpected error calculating that workflow's cost.
  • Fixed a bug when editing a Method Configuration that caused the cursor to move to the end of the field with every character typed.

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Tue 10 Jul 2018
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