Sanntis

[Marie59]

Add new tool for the marine Omics pilot of Fair-Ease. This tool (sanntis created by @SantiagoSanchezF) takes as an input the output of interproscan.
The aim here is to create a workflow using Interproscan then sanntis.

However, Sanntis also needs a genbank to function as an input. So the full workflow would be for instance:

1. Get a nucleotide fasta
   -> with 1. use prodigal get a protein fasta -> from this protein fasta use Interproscan and retrieve a tsv
   -> with 1. construct the Genbank
2. Take the tsv and the genbank and use them as input of sanntis

From there I still need to test if the pipeline works but on my side the sanntis tool itself seems to be working fine.

@bgruening and @yvanlebras Do you know of any tool that constructs Genbanks ?? If not @SantiagoSanchezF told me it should be easy to create a tool but it would for instance be only for this Prodigal example.

As you both know all this gene stuff is not my domain of expertise so, I hope I am clear enough ;)

What do you think of this ? Thanks !!

[bgruening]

bakta and prokka can create Genbank files. Those are genome annotation tools https://usegalaxy.eu/root?tool_id=toolshed.g2.bx.psu.edu/repos/iuc/bakta/bakta/1.9.3+galaxy0 however, it is for annotation of bacterial genomes, MAGs and plasmids. Is that what you need?

Prodigal in Galaxy can already output genbank files afaik: https://usegalaxy.eu/root?tool_id=toolshed.g2.bx.psu.edu/repos/iuc/prodigal/prodigal/2.6.3+galaxy0

[Marie59]

bakta and prokka can create Genbank files. Those are genome annotation tools https://usegalaxy.eu/root?tool_id=toolshed.g2.bx.psu.edu/repos/iuc/bakta/bakta/1.9.3+galaxy0 however, it is for annotation of bacterial genomes, MAGs and plasmids. Is that what you need?

Prodigal in Galaxy can already output genbank files afaik: https://usegalaxy.eu/root?tool_id=toolshed.g2.bx.psu.edu/repos/iuc/prodigal/prodigal/2.6.3+galaxy0

@SantiagoSanchezF what do you think of that ? Is this enough ?

[yvanlebras]

yes, in the example of sanntis, they are taking prodigal output genbank file as far as I know.

[bgruening]

I think the shed.yml needs some more love the rest is ok!

[Marie59]

I think the shed.yml needs some more love the rest is ok!

On it ;)

[Marie59]

Waouh a tool created and working in 2hours ! Me happy !! Thanks !!

[bgruening]

Get it into https://github.com/usegalaxy-eu/usegalaxy-eu-tools and its deployed tomorrow ;)

[Marie59]

oh in which section does it go ?... @yvanlebras would biodiversity exploration be okay ?

[yvanlebras]

hmmm I am not sure... It will be best in something related to "Annotation" with interproscan. So maybe choose "Annotation" AND add "ANNOTATION" tools section to ecology domain

[Marie59]

hmm okay will do If you want I can add ANOTATION only for the earth system domain
As you wish