ensembl-vep cannot be installed with arm64 (Apple Silicon)

[gernophil]

First of all thanks that more and more packages are available for arm64. ensembl-vep is available as noarch. However, it cannot be installed since neither perl nor perl-bio-db-hts is availble in the needed version for arm64. Could you make those available so I can install ensembl-vep into my arm64 conda?

% mamba create -n test ensembl-vep 

Looking for: ['ensembl-vep']

bioconda/osx-arm64 (check zst)                      Checked  0.1s
bioconda/noarch (check zst)                        Checked  0.1s
bioconda/osx-arm64                                  35.7kB @ 372.2kB/s  0.1s
bioconda/noarch                                      4.3MB @  11.8MB/s  0.4s
conda-forge/osx-arm64                               11.3MB @  25.4MB/s  0.4s
conda-forge/noarch                                  16.2MB @  29.1MB/s  0.6s
Could not solve for environment specs
The following packages are incompatible
└─ ensembl-vep is not installable because there are no viable options
   ├─ ensembl-vep [100.0|100.1|...|99.2] would require
   │  └─ perl >=5.26.2,<5.26.3.0a0 , which does not exist (perhaps a missing channel);
   └─ ensembl-vep [105.0|106.0|...|112.0] would require
      └─ perl-bio-db-hts >=2.11 , which does not exist (perhaps a missing channel).

[aliciaaevans]

Thanks for the request.

Perl is actually available on conda-forge from v5.32.*, but that message is because the solver was looking at older versions of ensembl-vep because it wasn't able to solve the latest version due to perl-bio-db-hts.

I tried building perl-bio-db-hts to see if it could be done easily. Unfortunately, looks like there are quite a few dependencies in the chain.perl-module-build is needed, which now lives on conda-forge: https://github.com/conda-forge/perl-module-build-feedstock so an issue or PR for osx arm should go there. perl-bioperl requires perl-bio-samtools which requires samtools <=0.1.17, which means we'd have to back build the older version(s) for osx-arm64 unless that constraint could be adjusted to 1.20 (which we could do, but I'm not sure what types of issues might be encountered).

I can't look more into it right now, but I want to leave this info here in case you or someone else wants to work on some of that.