We’re moving the GATK website, docs and forum to a new platform. Read the full story and breakdown of key changes on this blog.
Release Notes: April 2018
April 25, 2018
- We fixed a bug preventing users from creating clusters.
- You can now use R version 3.4 in your Notebooks.
- You can now see FireCloud's status in the application by clicking the "FireCloud Status" link in the footer of any page.
April 24, 2018
- When creating or cloning a workspace, you will now see that the dropdown for billing projects is in alphabetical order. (Previously, the projects were listed in arbitrary order.)
- Added a new endpoint to Sam to get the access token for a user's pet service account.
- The Swagger-UI interface here no longer requests OAuth scopes for Google Drive or Google Sheets
- You can now localize data URLs in addition to google bucket paths in Jupyter Notebooks.
- The Notebooks Dockerfile was unable to run; this has been fixed
April 18, 2018
- Free trial: A newly registered FireCloud user is automatically enrolled in the free credit program and will see the banner to start the trial as soon as they sign-in. New users are now getting $300 instead of $250 in credits too. Read more about this on the blog.
- Notebooks: You can now pause and resume clusters, which will help reduce your costs. The only cost is for storing the persistent disk in Google Cloud Storage, which is on the order of a single-digit $/month. The time taken to resume a cluster is a couple of seconds versus deleting it and spinning up a new cluster, which can take a couple of minutes.
- Profile: When you fill out your profile in FireCloud, your contact email can now include a plus character, + , without throwing any errors.
- Bug: Fixed a text rendering bug that could cause links stored in the Data tab or workspace attributes section to display their components out-of-order.
- Bug: Fixed a UI bug in the workspace attribute section that occurs when an attribute has embedded quotes in it (Ex. "\"hello\"").
- Bug: Reworked a piece of UI code that was causing undue load on the entire system.
April 10, 2018
- On certain datasets, submitting an analysis could trigger large SQL queries, resulting in other users experiencing "Lock wait timeout exceeded" errors on their own submissions. These SQL queries are now optimized and this known cause of database locks should be gone. We continue to look for any other causes of locks.
From time to time, FireCloud displays a popup indicating that the application is undergoing planned maintenance or is otherwise unavailable.
In this release of FireCloud, we have replaced the popup with a banner at the top of the screen. The banner behaves just like the popup used to - it appears automatically when the FireCloud web application cannot talk to its API server, and immediately disappears when the server is available again.
Additionally, you may notice that a screen you see when FireCloud is unavailable ("Error loading user information. Please try again later.") now displays a brief diagnostic message and status code. This information is designed to help the FireCloud team restore service as quickly as possible.
The automatic WDL parser in the Create New Method dialog gave nondescript error messages in some cases. This made it confusing as to whether the error was something in the WDL or something to do with FireCloud. Now, we've updated the error message to better indicate WDL as the source: e.g.
Error: WDL parsing failure. ERROR: Finished parsing without consuming all tokens <text from line it found error in>
- Consent has a concept of empty votes, where a DAC member has not yet voted "Yes" or "No". These empty votes could cause Consent to encounter an error when displaying a summary of vote outcomes. This error is now resolved.
- When logged in, you can now click the DUOS logo in the top-left corner of the screen to go back to the "Home" screen.
- Resolved an issue where certain less-common line endings prevented FireCloud from correctly previewing TSVs when importing data into a workspace.
- We now display an error message to you when there is an error during the consent match process. We have also improved the performance of the match process.
- We have implemented a bug fix in DUOS to disallow invalid updates of a consent's data use letter GCS location.
- In the last release we enabled subworkflow metadata. However, this has caused out-of-memory issues when expanding all subworkflows all the time. We are disabling this for now with a more permanent fix coming soon.
April 3, 2018
- APIs retrieving Cromwell Workflow Metadata now return subworkflow detailed metadata, when available.