cellarium-workflow command line tool with google batch support#2
Draft
sjfleming wants to merge 70 commits into
Draft
cellarium-workflow command line tool with google batch support#2sjfleming wants to merge 70 commits into
sjfleming wants to merge 70 commits into
Conversation
Author
|
Needs documentation |
Draft
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
1 participant
Add this suggestion to a batch that can be applied as a single commit.This suggestion is invalid because no changes were made to the code.Suggestions cannot be applied while the pull request is closed.Suggestions cannot be applied while viewing a subset of changes.Only one suggestion per line can be applied in a batch.Add this suggestion to a batch that can be applied as a single commit.Applying suggestions on deleted lines is not supported.You must change the existing code in this line in order to create a valid suggestion.Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be applied on multi-line comments.Suggestions cannot be applied while the pull request is queued to merge.Suggestion cannot be applied right now. Please check back later.
All kinds of fancy good stuff.
Supposedly has support for local, vertex ai, and google batch submissions.
I've been actively developing for google batch, as I find it a bit more flexible. The google batch backend has been tried and works.
Can be used to run a
cellarium-mltool on aNexusextract like thiscellarium-workflow submit-batch-component \ --tool hvg_seurat_v3 \ --subcommand fit \ --config default_configs/hvg_seurat_v3_train.yaml \ --machine-type n1-standard-16 \ --accelerator-type nvidia-tesla-t4 \ --accelerator-count 1 \ --git-sha fbd3ec172f8d40eb05004be1315501d3f2fd466e \ --extract-bucket gs://cellarium-nexus-file-system-3293a8/pipeline/data-extracts/czi_human_primary_gr300genes/extract_files