Jeremy

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

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.

Regards,

Curtis

From: galaxy-dev-bounces@lists.bx.psu.edu [mailto:galaxy-dev-bounces@lists.bx.psu.edu] On Behalf Of Jeremy Goecks
Sent: Wednesday, June 12, 2013 3:09 PM
To: Karen Chait
Cc: galaxy-dev@lists.bx.psu.edu
Subject: Re: [galaxy-dev] cuffdiff wrapper not synchronized with cuffdiff version

Hello,

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/libz.so.1: 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.

Best,