bcftools: error while loading shared libraries: libgsl.so.25: cannot open shared object file: No such file or directory

[eudesbarbosa]

Hello. I'm having some issue installing and running bcftools after the most recent release (v1.15). And pinning the package to the previous version doesn't help. I also tried asking the developers: samtools/bcftools#1698

Anyone faced something similar? Any hints on how to proceed?

Error:

bcftools: error while loading shared libraries: libgsl.so.25: cannot open shared object file: No such file or directory

Dependency difference
...works (from previous log ):

2022-03-03T14:32:50.9725381Z + gsl 2.7 he838d99_0 conda-forge/linux-64 3MB

...breaks (from current log):

2022-03-23T09:01:56.7405052Z + gsl 2.7.1 hd82f3ee_0 pkgs/main/linux-64 2MB

...also forcing gsl ==2.7 or gsl ==2.7.0 just leads to a different error message (log):

bcftools: symbol lookup error: /usr/share/miniconda/envs/__setup_conda/bin/../lib/libgsl.so.25: undefined symbol: cblas_ctrmv

[jmarshall]

The bioconda bcftools package has been built using the conda-forge gsl package.

Fairly recently, the defaults channel has started supplying up-to-date (in terms of version number) versions of gsl, but these are evidently not compatible with the conda-forge packages.

It appears that conda-forge's advice in this scenario is to use channel_priority: strict and ensure that conda-forge comes before defaults as per Bioconda's installation instructions.

[eudesbarbosa]

Thank you very much for the answer, it was very helpful!