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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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Does the Matrix service have what it needs to serve mouse matrices #641

Closed kbergin closed 5 years ago

kbergin commented 5 years ago

Create a test analysis bundle in integration env for Matrix Service testing. For Mouse Smartseq2. Share this bundle with Marcus Kinsella at CZI via email or HCA slack to see if the matrix service needs anything else to be able to run mouse data.

If they don’t need anything, ask for feedback on mouse analysis outputs for Optimus and SS2.

Why? The Matrix service may need more information, or changes to the mouse data outputs

Where to start? Talk to Nick/Kishori, and reach out to Marcus via Slack. Check if there is SS2 mouse example output bundles in a DCP environment. Work with Lantern to create them if there is not, it can be done before validation is complete, as long as it’s known it cannot be merged into Prod until it is validated].

When is it done? When the matrix service can support mouse data outputs, or when we have a list of task needed to complete matrix service support.

┆Issue is synchronized with this Jira Story

kbergin commented 5 years ago

➤ Charles Yan commented:

I think we’ll need to run ss2 on mouse inputs to create an analysis bundle for this. To do this we’ll need an ss2 mouse input bundle and mouse references for ss2.

kbergin commented 5 years ago

I was under the impression that Hornet already had the mouse references because [~accountid:5b43ab1e441e440653b0a4d9] had said that SS2 mouse was ready to go on the Hornet side as soon as we had validated. Let us know if you need reference info from us, though. Thanks Charley!

If you reach out in the wranglers channel on HCA slack you can probably find someone who can point you to a mouse primary bundle.

kbergin commented 5 years ago

➤ Charles Yan commented:

The infrastructure changes that came in after the pipeline surge set us up to be a step away from running mouse bundles for ss2, but not quite there. The outstanding steps are to trivially drop-in the mouse references and to modify lira’s subscription query for ss2 to include mouse bundles. I got the references from Kishori earlier today and have added them on a branch. I will merge that up once I’ve successfully run a mouse bundle through the pipeline.

kbergin commented 5 years ago

➤ Chengchen Wang commented:

The workflow failed at the submission: https://job-manager.caas-prod.broadinstitute.org/jobs/2106c2aa-e31a-4654-a289-d6b5dde3a356 ( https://job-manager.caas-prod.broadinstitute.org/jobs/2106c2aa-e31a-4654-a289-d6b5dde3a356 )

It seems the lira config for launching the workflow is a bit messed up, by using integration everywhere should work!

kbergin commented 5 years ago

➤ Charles Yan commented:

We’ve prepared an analysis bundle in integration now: analysis bundle uuid 51d8eda8-bbd9-48ab-9ffc-00cf1cdef087 analysis bundle version 2019-08-05T141528.848170Z primary bundle uuid c6cb322a-3d63-4a0b-8440-533da4febc63 primary bundle version 2019-08-02T202139.757537Z

kbergin commented 5 years ago

@mckinsel @brianraymor @jkaneria has matrix service had the chance to validate these bundles?

brianraymor commented 5 years ago

From my conversation with @mckinsel yesterday, the bundles were a-ok and our implementation is proceeding.

samanehsan commented 5 years ago

In that case, is it okay to close this ticket @kbergin?

mckinsel commented 5 years ago

fyi, we've closed the related ticket in the matrix service repo: HumanCellAtlas/matrix-service#279

samanehsan commented 5 years ago

Awesome! Thanks for the update @mckinsel!