Adding [email protected]

[almahmoud]

Adding [email protected]+galaxy1
Adding [email protected]

[natefoo]

@galaxybot test this

[natefoo]

Could you add this just to the usegalaxy.org toolset for now? We're not using the common toolset yet.

[almahmoud]

Done! Sorry for the delay

[natefoo]

This won't work until bioconda/bioconda-recipes#19790 is fixed, will it?

[bgruening]

@almahmoud I created already a fixed container. And to fix your tool on usegalaxy.org, copy the binary manually into your conda dir ...

[natefoo]

Copy from the biocontainer? Or is the binary available somewhere else?

[almahmoud]

@bgruening Are you referring to: quay.io/biocontainers/prokka:1.14.5--pl526_0? And would it be possible to patch this in: tseemann/prokka#451 to work with NFS?

[bgruening]

wget ftp://ftp.ncbi.nih.gov/toolbox/ncbi_tools/converters/by_program/tbl2asn/linux.tbl2asn.gz

@almahmoud, yes please test, this one should work hopefully.

[almahmoud]

Unfortunately, quay.io/biocontainers/prokka:1.14.5--pl526_0 does not work :/ (says it has old tbl2asn)
Update: I didn't realize the updated container was re-using an existing tag, and that image was already pulled on the machine. After deleting and re-pulling the old one, tbl2asn works, just need to add the patch tseemann/prokka#451 to work on NFS, otherwise the container works in other scnearios.

[bgruening]

bag@bag:~/projects/code/galaxytools/tools/rna_tools/graphprot$ docker run quay.io/biocontainers/prokka:1.14.5--pl526_0 tbl2asn
[tbl2asn] You must supply either an input file (-i) or an input directory (-p).
Use -p . to specify the current directory.

Seems to work for me.

[almahmoud]

I added just the newest (working) one for now to get a working prokka on Main in the meantime, until we add and patch the other one(s) as well.

[natefoo]

@galaxybot test this

[natefoo]

@galaxybot deploy this

[natefoo]

I also snuck tbl2asn updates in to the prokka 1.12 and 1.13 conda envs during this install.