Release Notes: January 2019

Posted by KateN on 4 Jan 2019 (0)

January 17, 2019


We have updated some of the libraries and packages that are pre-loaded upon creation of a notebook cluster on FireCloud. These changes will affect creation of NEW clusters ONLY; existing, paused clusters will not be affected.

The aforementioned updates, listed below, are expected to be compatible with existing libraries and packages with the exception of the Hail 0.1 to 0.2 upgrade; this change will be a breaking change*.

Version changes for libraries and packages:

  1. hail 0.1 --> 0.2
  2. python 3.4 --> 3.6
  3. R 3.4 --> 3.5
  4. pandas 0.22.0 --> 0.23.4
  5. numpy 1.15.0 --> 1.15.2
  6. google-api-core 1.3.0 --> 1.5.0
  7. google-cloud-bigquery 1.4.0 --> 1.6.0
  8. bokeh 1.0.0 --> 1.0.1
  9. table of contents extension for Notebooks will be installed by default

*Hail 0.2 has a new file format and cannot read Hail 0. You can learn more about the Hail 0.1 --> 0.2 changes here. If you need to create a new cluster with the Hail 0.1 version, please reach out to FireCloud support and we can help you to do so!

In the future, we plan to make it possible to enable access to prior versions of the notebook kernels when we roll out new upgrades to ensure long-term reproducibility.

January 15, 2019

FireCloud UI

  • Re-launched a user satisfaction (Net Promoter Score, or NPS) survey within the FireCloud UI.

January 10, 2019

FireCloud UI

  • A known google issue may cause the UI to report that a workspace bucket is unreadable, or there may be workflow failures. Refreshing or retrying manually will help, but while we wait for a more comprehensive fix from Google, we have added retry logic to help handle the issue.

January 7, 2019

FireCloud UI

  • When viewing the details of an individual workflow through the UI, the input and output values are now loaded on demand instead of preloaded. This update improves performance and reduces errors on the initial page view where previously, the payload was too large to handle.

January 3, 2019

FireCloud UI

  • Fixed a bug that prevented the viewing of an individual workflow, if the current workspace had a space in its name. This bug was introduced in the November 14, 2018 release. Thanks to @mbookman for identifying this bug.
  • The workflow timing diagram now shows a tooltip of "Running" for properly-running tasks. Previously, it incorrectly showed "Still Running when workflow ended" even though the workflow had not ended. This bug was introduced in the November 1, 2018 release.
  • In the Data Library, the column "Consent Codes" has been renamed to "Data Use Limitations".
  • To improve security, the FireCloud UI now incorporates protection from the tCell browser agent.


  • Some R packages were failing to install due to a system dependency. This has now been fixed.
  • Cluster scopes are now definable by the app/user.
  • Added new version end point for Leonardo.

Return to top

Fri 4 Jan 2019
Comment on this article

- Recent posts

- Follow us on Twitter



@jamesaeddy Going to phone a friend on that one — @geoffjentry care to explain?
19 Mar 19
Heads up if you use the TARGET and/or TCGA data workspaces: the file paths to TARGET and TCGA data are going to cha…
19 Mar 19
RT @lynnlangit: really love the sizing notebooks feature in @ProjectJupyter #Bioinformatics
15 Mar 19
To @harvardmed researchers and friends: Come meet, the platform that powers FireCloud and m…
13 Mar 19

- Our favorite tweets from others

The macaque genome isn't finished so it has over 200K contigs. I call them the Rhesus pieces.
15 Mar 19
It's been years in the making, but 500k structural variants (SVs) from 15k genomes in #gnomAD are out 🎉today🎉! Pre…
15 Mar 19
@fdmts @tanyacash21 and R. Munshi @broadinstitute are beginning their session on hype vs. reality in cloud capabili…
12 Mar 19
watching "Genomics TV" #bioinformatics #GATK @broadinstitute
5 Mar 19
“Running Containers — for Biologists” #Bioinformatics #Docker
4 Mar 19

See more of our favorite tweets...