Afif Elghraoui

Looks like someone created a project solely to do slurm job submission within Python: https://github.com/brentp/slurmpy

@mstud, thanks. We had a user request installation of slurmpy when we already had pyslurm installed, and I found out from this issue that submission isn't handled by pyslurm. I...

I'm not sure it would. My `06.fixstart.promer.promer` look like this: ``` PROMER [S1] [E1] [S2] [E2] [LEN 1] [LEN 2] [% IDY] [% SIM] [% STP] [LEN R] [LEN Q]...

you can verify the proper github link gets created from the rendering on my fork: https://github.com/0xaf1f/prokka/tree/doclinks#option---proteins

I just posted in https://github.com/tseemann/prokka/issues/614#issuecomment-1074803518 that there shouldn't be a need to pin to old versions anymore since Bio::SearchIO::hmmer3 is now in bioconda.

This became a problem since the Bioperl team decided to take Bio::SearchIO::hmmer3 (and a bunch of other things) out of the core distribution in v1.7.3 (). Suffering from this problem...

Locus tags are numbered incrementally in the genome, so SEQ0024 as you have it will always be the 24th gene in a given sample, which is usually not the same...

> Current version of BioPerl is 1.7.8. Are you saying go back and install BioPerl 1.7.2? @joneson this shouldn't be necessary anymore. See https://github.com/tseemann/prokka/issues/614#issuecomment-1074803518

For me, even with regular conda (I usually use the mamba resolver), it's getting the right packages. Maybe you need to refresh your package index with `conda clean -i`. :man_shrugging:...

The `CPATH` setting is necessary to find the hdf5 headers if they're not on the standard header search path. You need to also set `LIBRARY_PATH` to search the folder containing...