singlem container issue

[wwood]

Hi,

I'm not familiar enough with biocontainers to understand what is going on here, but it seems there is an issue in the singularity container, documented at https://github.com/wwood/singlem/issues/227 - you can likely reproduce following the instructions at #issuecomment-3025945761 except using the biocontainer one (there is an officially supported container, too, but I suppose that cannot be included as a biocontainer since it doesn't follow standard biocontainer practice).

Thanks in advance, ben

[mboudet]

Hello,

As the container is built from the conda package, you might want to create an issue on https://github.com/bioconda/bioconda-recipes (or ping on the gitter maybe).

As far as I can see, there are at least two issues, probably because the base docker image seems to be a busybox

• singlem appraise only seems to print a weird stdout + a nroff: command not found error, which I assume is the reason for the 'Pipe broken' issue you have.

• Trying to reproduce the error, I also have a sort: unrecognized option '--parallel=1' issue, probably because the 'sort' package with busybox does not have that option.

Not sure how to fix these with the bioconda environnement, you might have to ask the experts over bioconda.

[wwood]

Hi,

Thanks for sorting through this.

The sort issue was easy to address, just added the coreutils package to the conda spec. I haven't tested but assume it will be fixed for the next release.

The nroff one is harder - because there is no man-db conda package for linux. Is there one on busybox?

[mboudet]

I think the 'groff' conda package should contain nroff at the very least, but I'm not sure if that would be enough?