isPcr check failing when running in a container due to grep -P

[DarianHole]

Hi,

The isPcr check isPcr 2>&1 | head -1 | grep -Po "(?<=v )\S+" is failing when running in the https://depot.galaxyproject.org/singularity/el_gato:1.20.1--py311h7e72e81_0 singularity container

From testing, the issue appears to be that the container doesn't support the -P perl-extended regex flag used. Are you able to adjust it to accommodate that restriction? I had grep -o "v [0-9]\+x[0-9]\+" | sed "s/v //" and that seems to have worked in its place but it isn't as elegant a statement

Thanks,
Darian

[Alan-Collins]

Hi Darian,

Thanks for raising this issue! it's hard to beat the elegance of PCRE lookarounds, but it seems the singularity container version of grep supports extended regex so I change the command to isPcr 2>&1 | head -1 | grep -Eo "v \S+" | cut -d" " -f2 as that seemed simplest. We'll include this change in our next release.

Thanks!
Alan

[DarianHole]

Thanks Alan! That is very much appreciated