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.

Return to top

Tue 10 Jul 2018
Comment on this article


- Recent posts



- Follow us on Twitter

FireCloud

@BroadFireCloud

The analysis described in this paper is available in reproducible form in FireCloud; see https://t.co/uSChRZIoZg fo… https://t.co/j1zeh2TGRg
30 Nov 18
@xDBio_Inc @geoffjentry @WDL_dev @gatk_dev It’s pretty new, glad you like it! Think we should add the name itself a… https://t.co/65jwJEbyQu
23 Oct 18
We’re excited to deliver our #ASHG18 Invited Workshop on reproducible research tomorrow morning! Looking forward to… https://t.co/6vmB5qaA1H
17 Oct 18
RT @NCI_NCIP: Does @BroadFireCloud sound familiar? It should! @AllofUsResearch uses the same researcher workbench as this @NIH initiative.…
16 Oct 18
RT @broadinstitute: .@BroadGenomics put together a comprehensive list of @broadinstitute activities at #ASHG18. Find out about sessions, po…
16 Oct 18

- Our favorite tweets from others

The question is, how will @Microsoft and @Docker team up to solve collaborative challenges in the area of Bioinform… https://t.co/IKzElembVl
4 Dec 18
@geoffjentry Who doesn't love a Warp Pig? @WDL_dev and @gatk_dev are on the ball getting stickers out. Was happy to… https://t.co/91OODRpFOC
22 Oct 18
Does @BroadFireCloud sound familiar? It should! @AllofUsResearch uses the same researcher workbench as this @NIH in… https://t.co/8ZyoMBSG4x
12 Oct 18
Today at #GATK course, pipelining with WDL, Cromwell and Firecloud! @ClinicalBioinfo @FProgresoysalud @gatk_dev https://t.co/V4bLinpoPh
20 Sep 18
@dgmacarthur If anybody wants to sequence my genome to find the rare variant that is preventing me from going into… https://t.co/xGPGDZn9rQ
11 Jul 18

See more of our favorite tweets...