Integrate dsub #195
Integrate dsub #195
Conversation
Merge Reed Comp Bio SPRAS master branch
…mporary fix to use dsub as framework with oi1, change to gcloud storage cp for larger file transfers
…dsub file paths are handled in container command
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Some additional context: we started using dsub for All of Us
However
It's not yet clear what All of Us will do to support migration. I would still like to proceed with merging in this code though, but we may be okay keeping documentation light if our use case is already deprecated. See also #130. |
As Tony pointed out in the PR review, Google Cloud Life Sciences is being deprecated, so we're not sure how much longer this will be around. Instead of going through and giving the `dsub` framework verbose documentation, we explicitly state it's usage is experimental and warn the user that they should already know what they're doing if they plan to use it.
This prints a warning for the user if they select the `dsub` framework. Since we're unsure whether we'll need to support dsub in the future (as our primary motivation for using it is being deprecated), this warning should prevent potential users from getting their hopes up that we have long-term plans for it.
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@agitter, I believe @nisthapanda tested this integration with GCLS and verified that the merge didn't break anything for her. Since we're not sure what the long-term plan is for Since this isn't breaking tests in either direction, I think it's ready for a proper review. |
Opening this PR in draft mode for now while @nisthapanda work through collaborating on documentation updates and other testing.