I could not install htslib v1.12 with conda using either commands:
conda install -c bioconda htslib
conda install -c bioconda/label/broken htslib
Using conda install -c bioconda/label/cf201901 htslib gave me htslib v1.9.
Does anyone know how to install v1.12 with conda? Thanks!
The directives OP reference are from Anaconda Cloud, which are generic and miss the nuances that using specialized channels often entails. Specifically, Bioconda expects the following channel prioritization:
channels:
- conda-forge
- bioconda
- defaults
This is the order Bioconda uses when building and testing packages. Not following this can lead to undefined behavior.
Best practice is to either set this globally - great if you primarily work with bioinformatics software - or set it in an env-specific way (i.e., use conda config --env).
Otherwise, to mimic this channel priority manually one would use
conda install --override-channels -c conda-forge -c bioconda -c defaults htslib=1.12
but most of the time one can get away with
conda install -c conda-forge -c bioconda htslib=1.12