The singularity image pulled from docker://sangerpathogens/roary does not accept input gff files

[dawnmy]

Since conda failed to install roary, I switched to use singularity. I pulled the image with

singularity pull roary.sif docker://sangerpathogens/roary

But when I run the command:

singularity run pipelines/singularity/roary.sif roary -f outputs -e -n -v all_strains/*.gff -p 20

I got:

2024/02/19 16:58:50 Error: Cant access file all_strains/1.gff

I am sure all the gff files are in the all_strains dir and can be read

[cyanochic]

You may have already solved this since it's been a few months, but just in case you haven't. I use apptainer (essentially same as singularity) and I get this type of error when the container isn't allowed read/write access to that directory without additional options/flags. I fix this by adding --bind /path/to/directory/ after run.

[dawnmy]

Thank you so much for sharing the solution.