AFAIK, the requirements stuff is still work in progress?

Yes, of course you're right - there has to be a better way -
particularly where there are complex inter-dependencies like
weblogo/python/corebio

On Thu, Jul 7, 2011 at 10:41 PM, Holger Klein <h.kl...@imb-mainz.de> wrote:
> 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:
> https://bitbucket.org/galaxy/galaxy-central/issue/82/fix-the-tag-set-in-the-tool-configs
>
> 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?
>
> Regards,
> Holger
>
>
>
>
>
>>
>>
>> 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)
> http://www.imb-mainz.de/
> Tel: +49(6131) 39 21511
>



-- 
Ross Lazarus MBBS MPH;
Associate Professor, Harvard Medical School;
Director of Bioinformatics, Channing Lab; Tel: +1 617 505 4850;
Head, Medical Bioinformatics, BakerIDI; Tel: +61 385321444;

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