Workflow for trinotate

[Eduardo-Alves]

https://trinotate.github.io

• upgrade signalp wrapper to 4.0 hg clone https://toolshed.g2.bx.psu.edu/repos/peterjc/tmhmm_and_signalp
• Upgrade transdecoder wrapper to 3.0
  https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder

[Eduardo-Alves]

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.

[bgruening]

True, this was an issue :(

[lecorguille]

@bgruening Can we imagine pushing those developments under IUC repo and blacklist them https://github.com/galaxyproject/tools-iuc/blob/master/.tt_blacklist?

[bgruening]

The new signalp wrappers? Or what do you mean?

[Eduardo-Alves]

I checked the wrapper and it requires users to install the dependencies themselves. is this the approach we should take with software that requires license?

http://toolshed.g2.bx.psu.edu/view/peterjc/tmhmm_and_signalp

"First install those command line tools you wish to use the wrappers for:

Install the command line version of SignalP 3.0 and ensure signalp is on the PATH, see: http://www.cbs.dtu.dk/services/SignalP/
Install the command line version of TMHMM 2.0 and ensure tmhmm is on the PATH, see: http://www.cbs.dtu.dk/services/TMHMM/
Install the command line version of Promoter 2.0 and ensure promoter is on the PATH, see: http://www.cbs.dtu.dk/services/Promoter"

[lecorguille]

@bgruening Yes

[bgruening]

I'm very skeptical about the new SignalP version. We are not allowed to distribute it :(
@Eduardo-Alves this also applies for Docker containers, so we can not ship a functional tool inside of this container. We can add documentation to include the binary manually into our container during runtime. But during build time this is not possible. The first solution is not user friendly at all so I would vote for not including this tool in this container :(

[Eduardo-Alves]

looking at alternatives.
http://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-10-S15-S2

[Eduardo-Alves]

I found a few alternatives:
sigCleave is part of the emboss https://github.com/galaxyproject/tools-devteam/tree/master/tools/emboss_5
sigHMM (available for non-commercial use -- is this acceptable?) http://share.gene.com/share/zhang.wood.bioinformatics.2003/sighmm/index.html
PredSi (no restrictions) http://www.predisi.de/

PredSi performs best of the three according to the link in my previous post.

Any experience with these software? I need to check if the output is compatible with trinotate.

[bgruening]

No experience so far. I would avoid all strange licenses like the one from sigHMM. But PredSi sounds nice ... thanks for the research!

[Eduardo-Alves]

i wrapped PredSi and uploaded to testtoolshed
https://testtoolshed.g2.bx.psu.edu/view/eduardo/predsi/dda118a96cb0

[bgruening]

Nice this looks good! Do you want to put this into https://github.com/galaxyproject/tools-iuc. I can guide you through this process and help you creating conda dependencies.

[Eduardo-Alves]

Thank you Björn, please let me know how to do it

Eduardo

On Fri, Sep 30, 2016 at 4:32 PM, Björn Grüning [email protected]
wrote:

Nice this looks good! Do you want to put this into https://github.com/
galaxyproject/tools-iuc. I can guide you through this process and help
you creating conda dependencies.

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[bgruening]

@Eduardo-Alves have a look at this example: galaxyproject/tools-iuc#899

You more or less just need to create a PR against https://github.com/galaxyproject/tools-iuc I will review it and we can iterate until it is perfect :)

Thanks a lot!
Bjoern

[lecorguille]

WIP Trinotate wrapper: galaxyproject/tools-iuc#1030

[Eduardo-Alves]

Bjoern

I have moved predsi (signal peptide prediction )and two other tools (tmseg and dgpi) to my tools-iuc branch. they are under protein_annotation.

https://github.com/Eduardo-Alves/tools-iuc/tree/master/tools/protein_annotation
https://github.com/Eduardo-Alves/tools-iuc/tree/master/packages/package_predsi_2004_02_13
https://github.com/Eduardo-Alves/tools-iuc/tree/master/packages/package_tmseg_2_2_0
https://github.com/Eduardo-Alves/tools-iuc/tree/master/packages/package_dgpi_2_04

I also created a tools, mergegffs which works similar to trinotate: It loads a protein prediction gff and several annotations: blast, tmhmm, signalp, hmmer to a sqlite database using gffutils as you suggested during GCC2016.

https://github.com/Eduardo-Alves/tools-iuc/tree/master/tools/mergegffs
https://github.com/Eduardo-Alves/tools-iuc/tree/master/packages/package_genomegtftools_1_0 (this is a fork of the python package, I have the authors permission to wrap it and I will do a PR to his python repository with my changes)

The tools are working fine when installed from toolshed but I am getting an error in travis CL since it is using conda resolution only.

https://travis-ci.org/Eduardo-Alves/tools-iuc/jobs/219895680

UPDATE:
I managed to test using shed_test. Found some issues with mergegffs and working on it.

planemo shed_test --shed_target local --owner planemo --no_cleanup --galaxy_root /opt/galaxy/galaxy-app --tool_dependency_dir /opt/galaxy/galaxy-app/database/dependencies

Thank you

Eduardo