M Bernt

Just remembered `add_gff3_locus_tags.py`. But apparently some entries in the gff file dont get a locus_tag. I'm using this command line: `python3 gff/add_gff3_locus_tags.py -i ../juncus.fasta.transdecoder.refined.sort.gff3 -o ../juncus.fasta.transdecoder.refined.sort.lt.gff3 -p PREFIX -a 10`

Wonderful. Please send me a ping here, then I can try. I guess @arsilan324 can say about if the the counts of genes, mRNA, CDS, and exons are reasonable.

I looked around a bit: - ob_remSmall, ob_remDuplicates, ob_depiction_svg, ob_convert directly call babel which should be fine - ob_grep and multi_obgrep use obgrep: I tested successfully: `babel test-data/8_mol.smi test-data/8_mol.pdb; obgrep...

One more thing. If I got the xml file for convert correctly then for some output formats special options are set. Is the same done also for the infiles? Maybe...

I guess with a repeat the processing would be still sequential within one job. Which is more efficient (but not necessarily faster) in the sense that the overhead of creating...

One could even use this as FASTQ demultiplexer :)

As far as I see this repo is using 21.05 for testing PRs. So it should not be affected by https://github.com/galaxyproject/galaxy/pull/14332 which was for 22.01, or? Anyway, https://github.com/galaxyproject/galaxy/pull/14332 brought the...

Will be fixed in https://github.com/galaxyproject/galaxy/pull/14440

Thanks for checking @jennaj. This should be easy, unfortunately this does not work yet in Galaxy: https://github.com/galaxyproject/galaxy/pull/11754

Good idea. @jfallmann could you check if this also works with https://github.com/bgruening/galaxytools/pull/697 when breakmaf.sh is called and the parts are processed separately. I'm not sure if the warnings are still...