AlexsLemonade / AlexsLemonade/training-modules

Potentially update GSEA notebook gmt file handling

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1d 13h
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Description

The step to read in the GMT file in this notebook from a URL has been failing in GHA, even though this link is accessible and this code runs locally: https://github.com/AlexsLemonade/training-modules/actions/runs/25459583659/job/74821716126

If it turns out Broad is somehow now blocking this request from a GHA, we might want to get the file into a data/references directory first separately and have the notebook read from there. That said, we aren't going to be teaching this material for a little while, so we can also comment these notebooks out from running in GHA temporarily.

Contributor guide

Open the contributing guide

Research direction

Start by inspecting the failing GitHub Actions job and the GSEA notebook step that reads the GMT file from its URL. Determine whether the URL request fails only in GitHub Actions; done means the workflow handles the GMT data reliably, either from a repository reference location or by temporarily excluding the affected notebooks from the workflow.

Written by the indexing model from the issue text.

Assessment

Tech stack
github-actions, jupyter-notebook
Domain
bioinformatics, ci-cd
Issue type
Bug
Difficulty
3/5
Estimated time
1-2 days
Activity status
Quiet
Clarity
Mostly clear
Newbie friendliness
55/100

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