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TGAC / earlham-galaxytools

Galaxy tools and workflows developed at the Earlham Institute
https://tgac.github.io/earlham-galaxytools/
MIT License
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Update t_coffee to version 13.45.0.4846264 #139

Closed nsoranzo closed 3 years ago

nsoranzo commented 3 years ago

This replaces the t_coffee conda package (which used precompiled binaries and bundled methods) with the t-coffee one (which is compiled from source and uses other conda packages for methods).

This will fix https://help.galaxyproject.org/t/tcoffee-run-finishes-with-empty-results/3836 thanks to https://github.com/bioconda/bioconda-recipes/pull/25932 .

@anilthanki Can you test that all methods we expose in the tool UI still work? We may have to drop some of them, or add conda packages to the run requirements of the t-coffee conda package.

anilthanki commented 3 years ago

Tested it locally...

Works with and wothout filter options...

However, sap_pair in Pairwise Structual Method, throws warning saying its not installed, and uses TMalign instead.

And pcma_msa in Multiple Sequence Alignment Methods is not installed by defaults and ends up failing the analysis.

Also score_ascii, msf_aln and clustalw_aln output format doenst open withing Galaxy, but they downloads.

nsoranzo commented 3 years ago

Tested it locally...

Thanks for testing!

However, sap_pair in Pairwise Structual Method, throws warning saying its not installed, and uses TMalign instead.

https://github.com/bioconda/bioconda-recipes/pull/26079 https://github.com/bioconda/bioconda-recipes/pull/26092

Also score_ascii, msf_aln and clustalw_aln output format doesn't open withing Galaxy, but they downloads.

That's not connected to this PR, but we should change the format attributes of these <data/> elements to more general Galaxy datatypes (or added the datatypes to Galaxy, if it makes sense).

nsoranzo commented 3 years ago

And pcma_msa in Multiple Sequence Alignment Methods is not installed by defaults and ends up failing the analysis.

PCMA is not FOSS (non-commercial only), so we need to remove it. There's a huge list of other methods that should work and we could add, if there's interest.

nsoranzo commented 3 years ago

That's not connected to this PR, but we should change the format attributes of these <data/> elements to more general Galaxy datatypes (or added the datatypes to Galaxy, if it makes sense).

Corrected 3 output formats in commit 1358948d12cf0338d5a057ccd37b43e02f9d2676 , opened PR to add the missing msf datatype to Galaxy 21.01 in https://github.com/galaxyproject/galaxy/pull/11084 .

I've removed the amap_msa method (AMAP has been retired by its authors: http://pachterlab.github.io/software.html ) and added a few other methods more or less randomly from the long list of available ones.

There are 4 more methods that are failing among those exposed in the previous version: