A year in lockdown; 6 minutes of feature highlights

We’re seeing a lot of news features this week about the anniversary of the first coronavirus lockdowns in the US, from lighthearted takes on quarantine trends like hoarding toilet paper, baking sourdough, and sea shanties on TikTok, to much more serious reckonings of the dramatic and deeply unequal toll that this disaster has levied on our nation and the world. 

For those of us in the Broad Institute Data Sciences Platform, this is a time to take stock, but also to step away and allow ourselves to breathe. The Broad Institute has declared tomorrow, Friday 3/12, an Institute-wide holiday, which I expect will be particularly appreciated by our many team members and collaborators who have worked tirelessly both on the front lines and behind the scenes of COVID-19 response efforts.

For my part, the ambient retrospective mood inspired me to take a trip down memory lane, i.e. trawl through the release notes, to get a sense of how much functionality has been added in Terra since we formally switched to remote work a year ago. Turns out, there was a lot — including some things I wasn’t even aware of. This motivated me to compile a list of “actionable highlights”, focusing specifically on new options and capabilities that you would interact with in the user interface.

Assuming the last thing anyone wants is another slide deck to scroll through, I turned my list into two bite-size videos (3 mins each) dedicated to Interactive Analysis and Workflow Execution, respectively. You can find both videos embedded below and in the TerraBites playlist of the Terra YouTube channel, as well as a list of resources for learning more about the features they cover at the end of this post.

We’d love to hear your thoughts on whether this kind of feature roundup is helpful; if there’s enough demand we could do this on a more regular basis, perhaps quarterly. In the meantime, consider subscribing to this blog, the newsletter (which is a monthly digest of the blog content), or the Terra YouTube channel to get regular updates delivered to your inbox. 

Resources

Interactive Analysis 

• Available applications

• • Added RStudio (alpha) (blog)
  • Added Galaxy (alpha) (blog)
  • Notebooks: added Playground Mode (doc)

• Cloud environments (faq)

• • Persistent disks (doc) 
  • Built-in & custom cloud environments (doc)
    • Community-contributed environments (blog)
    • Roll your own (via Terra base container) (github)
  • Top 3 new packages pre-installed in built-in environments
    • Bioconductor (doc) 
    • AnVIL package (doc)
    • Seurat pre-installed in all R images (release note)

Workflow Execution 

• Cromwell capabilities

• • Deleting intermediate files (doc)
  • Task-level checkpointing (doc)

• Data sources 

• • Broad reference bundle on persistent disk (blog)
  • Creating entity sets on the fly (doc)
  • DRS integration (doc)

• Third-party 

• • Dockstore support for relative import paths (forum)
  • New WDL 1.1 features (specification)