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

sanger-pathogens / Roary

Rapid large-scale prokaryote pan genome analysis

http://sanger-pathogens.github.io/Roary

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Open dawnmy opened 4 months ago

dawnmy commented 4 months ago

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