Hi Ross,

On 07/07/2011 12:38 PM, Ross wrote:
> Holger, thanks for finding those errors - I'll take a look shortly.
> What's the 'dependency directory' ? I don't think the wrapper knows
> anything about it.

it's defined in universe_wsgi.ini:

# The directory containing tool dependencies
tool_dependency_dir = /local/data/home/galaxy/dependencies

We only recently installed galaxy locally, and Nate pointed me towards
this way to handle external tool dependencies.
This issue here is related:

Until now when tools didn't work with that mechanism (CCAT, clustalw) I
simply put a link into a directory which is in galaxy's path.

> The tool assumes that the weblogo script is on the path when the
> actual job starts executing - wherever that is.
> If the weblogo script produces output it must be on the path after you
> source that script and working I think.
> So, the environment on the execution node must include the relevant
> path. Otherwise it won't work.
> What path does the execution host get when a galaxy job is run?
> Does it include the right path to that weblogo script (marked executable)?
> Can the user each job runs as execute it?

I got a step further. The above mentioned mechanism with putting a link
to the weblogo executable simply into the path didn't work, because the
weblogo script uses the system-wide python (from #!/usr/bin/env python)
which doesn't have the corebio module installed. When changing the
interpreter to #!/home/galaxy/python/bin/python (galaxy-specific
virtualenv) it works. Somehow I just assumed that with setting the
PYTHON variable in the startup script would be sufficient.

So, now it works, but I wonder if there's a mechanism that is cleaner
than hard-coding the python interpreter? Is there a way to tell galaxy
or wrapper scripts to use a specific python version?


> On Thu, Jul 7, 2011 at 7:56 PM, Holger Klein <h.kl...@imb-mainz.de> wrote:
>> Hi Ross,
>> On 07/07/2011 02:07 AM, Ross wrote:
>>> Please try the new version 0.4 of the weblogo wrapper in
>>> galaxy-central #5772 - it has additional error reporting that may help
>>> clarify dependency or other problems and let me know how you go?
>> thanks, with the new version I get some more hints.
>> It seems that there is a problem with the path.
>> Just having weblogo installed in the dependency directory and using the
>> env.sh mechanism to set the path, the wrapper doesn't find the
>> executable at all:
>> --->%---
>> ## rgWebLogo3.py error - cannot locate the weblogo binary weblogo on the
>> current path
>> ## Please ensure it is installed and working from
>> http://code.google.com/p/weblogo
>> ---%<---
>> When I put a soft link to a directory which is in the galaxy user's
>> static path, I get a different error:
>> --->%---
>> Traceback (most recent call last):
>>  File
>> "/local/data/home/galaxy/galaxy-dist/tools/rgenetics/rgWebLogo3.py",
>> line 156, in
>>    checks,s = w.run()
>>  File
>> "/local/data/home/galaxy/galaxy-dist/tools/rgenetics/rgWebLogo3.py",
>> line 127, in run
>>    s = self.runCL()
>>  File
>> "/local/data/home/galaxy/galaxy-dist/tools/rgenetics/rgWebLogo3.py",
>> line 47, in runCL
>>    print >> sys.stderr, '## rgWebLogo3.py error - executing %s returned
>> error code %d' % cl
>> TypeError: not enough arguments for format string
>> ---%<---
>> Line 47 seems to lack the variable for the return code, when changing
>> the line to
>>             print >> sys.stderr, '## rgWebLogo3.py error - executing %s
>> returned error code %d' % (cl, rval)
>> I get the following message:
>> --->%---
>> ## rgWebLogo3.py error - executing weblogo -F png -c auto -o
>> /local/data/galaxy_files/000/dataset_304.dat -U bits -t
>> "Galaxy-Rgenetics Sequence Logo" -f
>> /local/data/galaxy_files/000/dataset_286.dat -s large returned error code 1
>> ## This may be a data problem or a tool dependency (weblogo)
>> installation problem
>> ## Please ensure weblogo is correctly installed and working on the
>> command line -see http://code.google.com/p/weblogo
>> ---%<---
>> So it still seems to boil down to my local weblogo installation.
>> Sourcing the respective env.sh and executing the above command line, I
>> get a valid png though (again with the warning mentioned before):
>> --->%---
>> galaxy@imbc1:~/tmp/1$ source ~/dependencies/weblogo/default/env.sh
>> galaxy@imbc1:~/tmp/1$ weblogo -F png -c auto -o
>> /local/data/galaxy_files/000/dataset_304.dat -U bits -t
>> "Galaxy-Rgenetics Sequence Logo" -f
>> /local/data/galaxy_files/000/dataset_286.dat -s large
>> /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
>> ---%<---
>> Could this be related to the way galaxy is setting the paths dynamically
>> using the env.sh file? Do I have to adjust python paths in there as well?
>> Regards,
>> Holger
>>> On Tue, Jul 5, 2011 at 5:49 PM, Holger Klein <h.kl...@imb-mainz.de> wrote:
>>>> 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.kl...@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

Dr. Holger Klein
Core Facility Bioinformatics
Institute of Molecular Biology gGmbH (IMB)
Tel: +49(6131) 39 21511
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