Lee Katz

cpanm --installdeps

3

Related to #456: How do I install modules listed in my Makefile.PL? Normally `cpanm -l . --installdeps .` works for me normally but I would like to see the recommended...

seq comp documentation per #47

1

https://github.com/lh3/seqtk/issues/47

GFF?

4

Does anyone have a nice one liner to get GFF out of abricate output?

Documentation requested for all output files

3

Not all files are described when I used `--keepfiles`. Could there be documentation for them, even if it's not in the main documentation? The additional files are the files I...

No need to load all assemblers

1

Sorry if this is a nonissue but I _think_ that Shovill requires all assemblers (skesa, spades, megahit) to be loaded in `check_deps`. If all dependencies are not loaded, then it...

samclip not fix-mated

1

per this issue, it looks like samclip needs to be followed by `fixmate`. https://github.com/tseemann/samclip/issues/7

bioperl v1.7.8 kills the prokka 🐿🔫

1

Prokka checks for bioperl >= `1.0006002` numerically using this code on line 257. ``` my $minbpver = "1.006002"; # for Bio::SearchIO::hmmer3 my $bpver = $Bio::Root::Version::VERSION; msg("You have BioPerl $bpver"); err("Please...

[bactopia-tool] cgMLST and wgMLST

2

**Related To** - [ ] Bactopia - [x] Bactopia Tools **Is this related to a problem?** Now that we have core genome MLST (cgMLST) and whole genome MLST (wgMLST) methods...

Hi guys, I thought that you might like this xargs example and so I suggested a way of running it in your readme. This is actually how I run FastANI...

Would you be willing to accept a Rust example by either myself or @hcdenbakker? Or, if you have the time to make one of your time-efficient functions...?