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HumanCellAtlas / secondary-analysis

Secondary Analysis Service of the Human Cell Atlas Data Coordination Platform
https://pipelines.data.humancellatlas.org/ui/
BSD 3-Clause "New" or "Revised" License
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Update Optimus in Terra with latest release #688

Closed kbergin closed 5 years ago

kbergin commented 5 years ago

We have v1.0.0 of Optimus in a featured workspace in Terra. It is off of this branch in skylab. It is on a separate branch because it has http imports instead of relational, a bumped up memory setting on the STAR task (is that part of the default workflow now?) and some additional test inputs (not sure why?).

We want to make the latest version of Optimus available to our users. We should update the workspace to point to the new release, and add test data and reference materials for Mouse support.

Where to start: With Bhanu or Sushma, updating the 

terra-optimus

branch in skylab with the latest version (keep in mind imports); dockstore, workspace Kylee, Tiffany Miller, or Tim can help you with access to the workspace or billing accounts. Hornet team can help point us to the mouse ref in production.

AC:

branch)

Nick reports that the workspace currently isn’t working, so we should investigate why/fix it.

┆Issue is synchronized with this Jira Dev Task

kbergin commented 5 years ago

➤ Nick Barkas commented:

Sushma was able to find the trick to get arrays of inputs to be processed. In the meanwhile the mouse test subsetted dataset was ready. I have updated both datasets (human and mouse) to be test datasets that will produce output matrices (chr21 and chr19, respectively). I am currently running both datasets in Terra. Once these are complete the workspace can be renamed and the ticket closed.

kbergin commented 5 years ago

➤ Nick Barkas commented:

The human dataset run ok, the mouse failed due to it being pre-empted multiple times. I put it to run again, but I expect that it will complete correctly.

kbergin commented 5 years ago

➤ Nick Barkas commented:

This is complete, I’ve asked [~accountid:557058:7f318d05-6e5c-4289-a9e0-ef0441bd7e57] for review.

The workspace is here: https://app.terra.bio/#workspaces/featured-workspaces-hca/hca_optimus_testing_development ( https://app.terra.bio/#workspaces/featured-workspaces-hca/hca_optimus_testing_development )

Please note that due to a bug in Terra the index files (or any other optional file arrays, can’t be processed correctly). This doesn’t affect functionality, I’ve raised this with Sushma who is escalating it as appropriate.

kbergin commented 5 years ago

[~accountid:5be1941dc9cd504f86cfde4c] I need you to share the workspace with me

kbergin commented 5 years ago

➤ Nick Barkas commented:

QA Instructions:

  1. Go to terra: https://terra.bio/ ( https://terra.bio/ )
  2. Find the workspace called “hca_optimus_testing_development”
  3. Read the documentation and make sure it makes sense
  4. Make sure you can clone the space (as any other user would do)
kbergin commented 5 years ago

➤ Jessica Way commented:

Documentation looks good and cloning was successful 👍