First of all, thanks for all your efforts, and for updating the cuffdiff, etc, 

However, it's a little frustrating to us that a non-backward compatible change 
in the supported version of the cuffdiff executable was not reflected in a new 
version number for the cuffdiff (and other cuff) wrappers. This leaves us no 
way to support both versions of cuffdiff, and makes all histories that were run 
with the older version "non-reproducible".

I know the general versioning problem is address through the tool-shed 
mechanism, but for the remaining core wrappers, can maintainers please update 
wrapper version numbers when making changes?

For this wrapper set, how would you advise us to support both?

It seems to me that I HAVE to leave the cuffdiff v1.3-compatible as 
wrapper_version=0.0.5, or old histories/workflows break.
However, if I change the cuffdiff_v2.1-compatible wrapper to something else, 
I'll be out of sync with galaxy-central, and will create 
migration/reproducibility issues in the future.

Would you accept a pull request to update the version number of the cuff 
wrappers that were changed in the migration to cuff*2.1?

Thanks again for updating the wrappers, and help me figure out how to support 
them cleanly.


[] On Behalf Of Jeremy Goecks
Sent: Wednesday, June 12, 2013 3:09 PM
To: Karen Chait
Subject: Re: [galaxy-dev] cuffdiff wrapper not synchronized with cuffdiff 

After the latest update of Galaxy I saw that the cuffdiff wrapper is for 
version 2.0. I updated the $PATH to cuffdiff v. 2.0.2 but when I run cuffdiff 
in Galaxy I get the following error:
Error running cuffdiff. cuffdiff: /lib64/ no version information 
available (required by cuffdiff)
cuffdiff: unrecognized option '--library-norm-method'
cuffdiff v1.3.0 (3022)

What else do I need to define inorder to run the latest version of cuffdiff.

This depends on your setup. If you're running Galaxy under a particular user, 
you may have to update that user's $PATH. If you're running on a cluster, 
you'll need to ensure that the submission script uses the correct $PATH.

If you provide more details on your set up, it may be possible to provide 
additional insight/suggestions for your problem.


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