ci: install bcftools explicitly in test workflow - #38
Merged
Conversation
bcftools is listed in environment.yml but was missing at test time, likely due to a stale cached environment. Install it explicitly after micromamba setup and verify the binary resolves.
Up to standards ✅🟢 Issues
|
Restored environment caches kept the conda package metadata but lost files on disk, so bcftools was reported as already installed while libgsl.so.25 was missing at runtime. A fresh solve of environment.yml correctly pulls bcftools 1.24 with gsl 2.7, which provides that library. Drop the explicit bcftools install added previously (a no-op against a corrupt env) and replace it with a version check that fails fast. Package download caching is kept.
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
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Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be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.
bcftools is listed in environment.yml but was missing at test time, likely due to a stale cached environment. Install it explicitly after micromamba setup and verify the binary resolves.