Hi Ross,
thanks for taking care of this issue.
On 07/05/2011 12:31 AM, Ross wrote:
Is this error seen on Galaxy main or test? If so please share the history with me so I can see the input and reproduce what sounds like a wrapper error?
Otherwise, if this is on a private instance, and if the tool has never produced output successfully, then this may be a dependency installation problem - eg you may need to ensure that the weblogo3 executable is available and working correctly on the path used by your execution nodes. To assure yourself that your data works with the tool, please try running it on main using the same data, and let me know what you see?
in fact it's a private instance of galaxy, it's the latest version of galaxy-dist (hg summary: 5743:720455407d1c). The input data is fine, it's a clustalw alignment in fasta format which can be used by the weblogo module on galaxy main.
Maybe some background info on the weblogo installation helps: it's located below the tool_dependency_dir as defined in universe_wsgi.ini in weblogo/3.0 (with default as a link to 3.0). It contains the file env.sh which sets the PATH: export PATH=/home/galaxy/dependencies/weblogo/3.0:$PATH
Starting the weblogo executable with the galaxy virtualenv python seems to work (just tested --help), although it returns a warning:
~/python/bin/python ./weblogo --help/home/galaxy/python/lib/python2.6/site-packages/CoreBio-0.5.0-py2.6.egg/corebio/seq_io/_nexus/__init__.py:19: DeprecationWarning: the sets module is deprecated import sets
I also tested putting a link to the weblogo executable in the PATH that's defined for the galaxy user (as opposed to the dependency dir mechanism, that I have to admit I don't fully understand yet), but that also doesn't work. Could this be an issue of PYTHONPATH needing to be adjusted?
Regards, Holger
Thanks again.
On Tue, Jul 5, 2011 at 12:34 AM, Holger Klein h.klein@imb-mainz.de wrote:
Dear all,
I have a problem with the weblogo tool. I have a clustalw alignment in fasta format that I'd like to visualize as a logo. The sequence logo module ends with a success (green box), the info tells me the amount and length of the input data. But the output is empty, there are no plots (no matter if I select jpg, png, pdf or text). The respective image can't be displayed "because it contains errors" or is empty in case of text.
I suspect that the actual call of the weblogo tool doesn't succeed, but I didn't figure out yet on how to check this. Does anybody have hints on where to look?
Cheers, Holger
-- Dr. Holger Klein Core Facility Bioinformatics Institute of Molecular Biology gGmbH (IMB) http://www.imb-mainz.de/ Tel: +49(6131) 39 21511 ___________________________________________________________ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list:
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