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ci: install bcftools explicitly in test workflow - #38

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cokelaer merged 3 commits into
sequana:mainfrom
cokelaer:main
Jul 23, 2026
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ci: install bcftools explicitly in test workflow#38
cokelaer merged 3 commits into
sequana:mainfrom
cokelaer:main

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@cokelaer

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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.

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.
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cokelaer added 2 commits July 23, 2026 14:13
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.
@cokelaer
cokelaer merged commit a0394bb into sequana:main Jul 23, 2026
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