Trinotate in Galaxy

[lecorguille]

Hi Eduardo,
We met briefly at Bloomington during the GCC.

We are interesting in a wrapper for Trinotate. There is no one visible in the ToolShed.
What I obtain in Google with "Trinitate Galaxy", is your repository about your visualization tool for Trinitate output.

But do you have a wrapper for Trinitate?

If not, we plan to implement one 😄

Cheers

[Eduardo-Alves]

Let's work together on it. I'm also working on porting the dependencies and
migrating the visualization part to a galaxy compatible db
On Sep 25, 2016 20:31, "Gildas Le Corguillé" [email protected]
wrote:

Hi Eduardo,
We met briefly at Bloomington during the GCC.

We are interesting in a wrapper for Trinotate. There is no one visible in
the ToolShed.
What I obtain in Google with "Trinitate Galaxy", is your repository about
your visualization tool for Trinitate output.

But do you have a wrapper for Trinitate?

If not, we plan to implement one 😄

Cheers

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[Eduardo-Alves]

first step are the dependencies
galaxy-genome-annotation/docker-galaxy-genome-annotation#5
but signalp 4.0 requires a license. we may have to stick with 3.0 which is wrapped already
https://toolshed.g2.bx.psu.edu/repository/browse_repository?id=292389a45f1a238a
I will test loading the db with results from signalp 3.0 today and see if it works.

[lecorguille]

I think all versions of SignalP are under Licence and can't be provide through Conda package officially.
And I was thinking about that. I wanted to push Trinotate under the IUC flag. So we can't integrate SignalP or TMHMM within Trinotate if we want to pass fonctionnal test.

But maybe, we can just aggregate outputs from existing wrappers. It's less practical for end-user, they will have to launch all the upstream steps separately. But it's more "Galaxy" to have atomic tools.

[Eduardo-Alves]

We can create a trinotate wrapper that is independent of the tool used for signal peptide prediction. This way if the user has a standalone signalp it can use its output but otherwise can use the output of a galaxy tool that produces predictions in the same format. I think we will have to do the same for transmembrane prediction

[lecorguille]

👍
Are you ok if I do it in IUC repo?
I think it will be really easy LOAD LOAD LOAD 😄

[Eduardo-Alves]

Bjorn suggested using gffutils to load the sqlite dB so that we are not tied to trinotate loaders and queries. This will simplify the development of the visualization component and can be used by other tools. If you want the trinotate loader only, wrapping the existing loader might be the way to go.