Cuffdiff SQLite output problem

[jennaj]

Update to 2.2.1.5 (from early 2017, conda updated). The server currently has 2.2.1.3 (2015).

https://toolshed.g2.bx.psu.edu/view/devteam/cuffdiff/d3ae7d9c2202

Duplicated posts at Biostars about the issue have all been consolidated into this post. Use as the master when helping users. Should also post back an update once resolved: https://biostar.usegalaxy.org/p/26894/

@natefoo @davebx

[natefoo]

This is done on Test and Main.

[jennaj]

Update: More tests running. Looks like there might be a problem with the SQLite option but I am confirming that.

[jennaj]

@natefoo Revised tests produce this

• SQLite option works with the earlier version 2.2.1.3

• SQLite option fails (alone) with latest version 2.2.1.5

The same data was used with both versions. This looks like a tool problem but could possibly be config/dependencies.

Error:

.... bunch of the usual log file lines ....

There were 50 or more warnings (use warnings() to see the first 50)
Creating database ./cummeRbund.sqlite
Reading Run Info File ./run.info
Writing runInfo Table
Reading Read Group Info  ./read_groups.info
Writing replicates Table
Reading Var Model Info  ./var_model.info
Writing varModel Table
Reading ./genes.fpkm_tracking
Checking samples table...
Populating samples table...
Error: Column name mismatch.
In addition: There were 50 or more warnings (use warnings() to see the first 50)
Execution halted

[jennaj]

@nekrut @bgruening

I noticed that Cuffdiff (and most Cuff* tools) are marked as deprecated at https://galaxy.uni-freiburg.de (all versions, including 2.2.1.5).

Should we remove Cuffdiff version 2.2.1.5 from https://usegalaxy.org?

And mark the earlier versions as deprecated? (Seem to work Ok)

Leaving the version that doesn't work on the main server is going to trigger more usage errors/bug reports. We have 9 so far sent to our bugs mailing list (since Feb 27th, when we updated) and a few other questions about the problem at Biostars (local use, public server use, example: https://biostar.usegalaxy.org/p/25358/ && https://biostar.usegalaxy.org/p/26894) that go back at least 4 months (the tool was last updated in the MTS about a year ago https://toolshed.g2.bx.psu.edu/view/devteam/cuffdiff/d3ae7d9c2202).

[bgruening]

@jennaj this deprecation warning was more a hint to our users that people should use other tools or get in contact with us. We do have some bad experience with cuff* and think people should use other tools if they can. However, a few users are still using them but we wanted to make clear that we will phase out these tools.

[jennaj]

@bgruening Ok, thanks! Then maybe the SQLite option not working is a https://usegalaxy.org problem. We've had that before and some config change @natefoo made fixed it. Looks like we need that again to get the tool fully functional. More bug reports have come in about this option/version - the latest was lasts night.

[jennaj]

ping @davebx @natefoo -- what is the status for the SQLite output fix? It might be the same as the prior correction for the same problem with earlier tool versions (problems were a server-side configuration issue if I am remembering correctly).

Thanks!

[jennaj]

Ignore the htseq link, mistake and unrelated.

Retesting Cummerbund again.

[natefoo]

Is there an updated version that fixes the SQLite output? If this is not a tool problem I am pretty unclear on what the issue is.

[martenson]

The Main server has the Galaxy Version 2.2.1.5 which is the latest in the MTS.

[jennaj]

I opened at ticket at devteam repo - this has been a problem for a while now, maybe the tool itself is buggy if the MTS install is Ok.

galaxyproject/tools-devteam#509

[jennaj]

devteam repo ticket updated -- tool still fails at ORG, testing at EU, details there

[jennaj]

Works at EU.

Is something different about the tool configuration?

@abretaud also reported a problem at his Galaxy, so should share the solution with him. galaxyproject/tools-devteam#509 (comment)

[jennaj]

Tool has been deprecated, closing.