containers picard locale issue

Hi there, I am unable to set the locale in the picard container from quay.

Steps to reproduce: docker run quay.io/biocontainers/picard:2.18.27--0 picard

/usr/local/bin/picard: line 5: warning: setlocale: LC_ALL: cannot change locale (en_US.UTF-8): No such file or directory USAGE: PicardCommandLine [-h]

I've also seen this converting this image to a singularity container. Since the container has been stripped of tools the issue cannot be resolved by the user.

Alexis

Mar 13 '19 05:03 alexiswl

Can you open issue on bioconda recipe?

@bgruening this may be a more global issue regarding locale setup on bioconda containers.

Mar 13 '19 06:03 osallou

Yes, locales are not part of busybox and are not supported. It would make the container significantly bigger than it is now. However, if a tool needs to have it, we can enable an extended-base-image in the meta.yaml of conda that will create a larger image but with locales available.

Mar 13 '19 06:03 bgruening

Thank you for the quick response, happy to close. I was able to create the container through the miniconda3 base image and rebuild the locales from there. Approx container size was 478 Mb in the end, which isn't too bad.

Alexis.

Mar 13 '19 11:03 alexiswl

@alexiswl would be great if the containers is publish througth conda the corresponding conda recipe as @bgruening suggested.

Mar 13 '19 11:03 ypriverol