FireCloud is now powered by Terra! -- STARTING MAY 1st, 2019 THIS WEBPAGE WILL NO LONGER BE UPDATED.
From now on, please visit the Terra Help Center for documentation, tutorials, roadmap and feature announcements.
Want to talk to a human? Email the helpdesk, post feature requests or chat with peers in the community forum.

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May 1, 2019

The user interface has been updated to direct you to Terra. You will have the option to opt-out of the redirect and continue using FireCloud. If you choose this, please fill out the question in the opt-out modal so that we can better understand how to make your transition easier.

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Release Notes: April 2019

Posted by SChaluvadi on 11 Apr 2019 (0)


April 24, 2019

  1. Cromwell release to update from Cromwell 39 to Cromwell 40. Full details listed here.

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In case you haven't met us yet, Beri and I (Sushma) are part of the Frontline Support Team here, aka the real humans behind the FireCloud and Terra forums and helpdesk. We're on deck every day answering questions and helping troubleshoot problems, so we have plenty of opportunity to get real friendly with both platforms - it comes with the territory. What you may not know is that we actually use FireCloud and Terra to create and maintain many of the Featured Workspaces, which on any given day might involve managing data, writing WDL workflows or hammering out some R or Python code in a Jupyter notebook. That's why we'll always be super sympathetic if you reach out to us; we've literally felt the same sink-back-into-your-chair frustrations as you at some point. On the flipside, we figure that when we feel joy or relief at some newly released feature that makes our work easier, that means you probably will too!

So we were talking about the upcoming transition from FireCloud to Terra, and we figured that we should share our unanimously favorite features, mighty or small, that didn’t exist in FireCloud but have really revolutionized our ability to get things done in Terra.


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Summary

We're planning to upgrade one of the main servers at the heart of FireCloud in order to unlock some performance enhancements ahead of a training event that is taking place later this week. We plan to perform this operation between 6:30-7am EST on March 20, 2019 and expect it should take about 5 to 10 minutes to complete.

Impact

  • For the duration of the upgrade process, it won't be possible to log into the application, and it's very likely that any API calls will either timeout or fail.
  • Actively running workflows should not be impacted but querying of status will timeout or fail.

For more information

If you would like to be notified of all service incidents or upcoming scheduled maintenance, click Follow on this page

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Heads up if you use the TARGET and/or TCGA data workspaces: we're planning an update that will change the paths to the data files. This will disable access to the original files in any clones of the original workspaces that retain the old paths, and it will affect call caching in any new clones of the original workspaces that you create after the update rolls out in a few weeks.

Read on to understand what this change entails and why it's an important improvement that is worth making.


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Release Notes: March 2019

Posted by SChaluvadi on 13 Mar 2019 (0)


March 12, 2019

Notebooks

  1. We have upgraded Hail to 0.2.10. This requires a cluster rebuild to take effect.
  2. We now set a lifecycle policy on clusters' staging buckets after the cluster is deleted. This helps control storage costs in users' billing projects.
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Last month we were excited to announce that FireCloud is getting a big upgrade, including a new and improved user interface called Terra. As a reminder, going forward we'll use the name “Terra” to refer to the overall platform that you use to get your work done, while “FireCloud” will refer to the NCI-sponsored project page that features TCGA and TARGET data. You can already access Terra here if you have a FireCloud account, and you may have received an email invitation to check it out.

Today we're following up on that announcement with some important news: the "classic" FireCloud portal will be turned off on May 1st. At that point, all traffic to FireCloud will be automatically redirected to Terra.


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We are excited to announce that we’re rolling out a new and improved user interface that addresses much of the feedback you’ve shared with us over the past three years. Using the new interface will not require you to change anything and should make doing research easier than before.


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February 27, 2019

FireCloud

  1. The Terms of Service API has updated its library dependencies, to proactively address security vulnerability warnings.

Notebooks

  1. A bug fix to address an issue where the token refresh that runs as a Jupyter extension was not running Lab, which was causing user tokens to expire and resulting in 401 errors. The workaround for this was to have a Terra notebook (not lab) open in a different tab while using Jupyter Lab which will no longer be needed.

Cromwell

  1. A new version of Cromwell, version 36.1, has been released with details listed here. Cromwell version 36.1 is an interim to Cromwell 37 containing many of the same features while small bug fixes are being resolved in v37.

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Release Notes: January 2019

Posted by KateN on 4 Jan 2019 (0)


January 17, 2019

Notebooks

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.


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