Update Trinity once in MTS to capture a new tool wrapper in the suite

[jennaj]

PR: galaxyproject/tools-iuc#1937

Related Q&A: https://biostar.usegalaxy.org/p/28312

[jennaj]

In progress by @davebx and @natefoo

[jennaj]

Trinity itself has been updated and more tools from the suite are in the MTS (and at usegalaxy.eu).

Do we want to add those to main? Can we even use those same versions at main? (not sure) @nekrut @natefoo

[jennaj]

Related request from the community (CTAT tools): #184

[jennaj]

Older ticket left over in galaxy repo (closed out). Punchline: the updated tool is ready to install. galaxyproject/galaxy#4418

[jennaj]

Tools are installed but the older version is still present. Both work. Before closing this out -- do we really want both versions available? And in different tool categories? It seems confusing for end-users.

IF we want Trinity under "Assembly" instead of "RNA-seq", then all Trinity/CTAT tools should be moved, so all are kept together.

Also: The old/new versions are not linked as usual under the Versions tool form menu because it is from a different tool suite/repository. @mvdbeek said he may be able to help with that.

Screenshot

ping @natefoo @davebx

[jennaj]

per @natefoo -- simply hide the old version and call it done for now.

who can do this? would be very nice to wrap this up and closeout :)

[jennaj]

Updates:

• Trinity has updated to an even newer version. v2.8.5 was tested and passed on Feb 19th. v2.9.1 is the new version tested today, April 3rd.
• All versions of Trinity reliably fail as of a day or so ago with the same error, see below.
• Not sure why "Detected Common Potential Problems" states that a duplicated dataset was input --- it definitely wasn't.
• The original Trinity tool is still in the tool panel. Not marked as deprecated, in a different tool group, does not thread vs "Version" to the updated wrapper. Hide or tag as deprecated? It is very confusing for end-users, and the old trinity wrapper's output does not play well with the updated Trinity tool suite (there are several downstream tools for filtering, annotation, expression, etc).

Test history, see the top 4 runs for today's tests, bit further down for Feb test. All tagged for context: https://usegalaxy.org/u/jen/h/test-history-trinity

GUI "bug" error reporting view's content below. srderr is included. stdout from Job Details view is blank (expected).

Dataset Error
An error occurred while running the tool toolshed.g2.bx.psu.edu/repos/iuc/trinity/trinity/2.9.1.

Error Details
Tool generated the following standard error:

code 17: slurm_submit_batch_job error: Invalid account or account/partition combination specified

Detected Common Potential Problems
The tool was executed with one or more duplicate input datasets. This frequently results in tool errors due to problematic input choices.

ping @natefoo I know we already discussed and you are working on this. posting to ticket for our tracking and sharing situation with end-users.

[jennaj]

Spades is reporting the same exact error. No other tools reported as bugs have the same error, and it only started on April 2nd (yesterday). See existing test history for an example.

Dataset Error
An error occurred while running the tool toolshed.g2.bx.psu.edu/repos/nml/spades/spades/3.12.0+galaxy1.

Error Details
Tool generated the following standard error:

code 17: slurm_submit_batch_job error: Invalid account or account/partition combination specified

[natefoo]

The errors were related to cluster upgrades and the exhaustion of our XSEDE credits for Bridges. I have hidden the old version of Trinity and am running a test of the new version, but don't have super high hopes for it because it's going to run on Stampede2 now instead of Bridges until we get a new allocation or supplement.

[jennaj]

Resolved!