samtools: no Perl in the container, tools fail to run

[lgorenstein]

Looks like Samtools containers is missing Perl, so many installed tools fail to run (blast2sam.pl, bowtie2sam.pl, etc):

$ singularity run https://depot.galaxyproject.org/singularity/samtools:1.9--h10a08f8_12 blast2sam.pl
WARNING: Skipping mount /var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container
env: can't execute 'perl': No such file or directory

Hopefully an easy fix, right?

[osallou]

Hi, this container is built from bioconda package, so if perl is needed, issue should be created on conda package (which will fix the container...)

Thanks

[lgorenstein]

Thank you Olivier, created an issue there.

[bgruening]

Commented upstream.