Oops sorry, meant to keep the list cc'd - resending.

On 18 March 2013 16:18, Clare Sloggett <s...@unimelb.edu.au> wrote:

> Hi Rob,
>
> Were you using a very old version of the library and examples or was it
> quite recent? In any case, try grabbing the script from
> https://github.com/afgane/bioblend/tree/master/docs/examples , we have
> done a lot of bugfixing and documentation recently. If you just want to
> test your setup there are also now some much simpler, less end-to-end
> example scripts that don't use any admin permissions, and we'll add a few
> more.
>
> The create_library step is the step where you're going to run into
> problems if you don't have admin rights to the Galaxy instance. If you're
> running on localhost though you should be able to set up the account as an
> admin account.
>
> Finally... we've put up some much better docs on using workflows (and
> libraries) in bioblend, which might be useful:
> http://bioblend.readthedocs.org/ and specifically
> http://bioblend.readthedocs.org/en/latest/api_docs/galaxy/docs.html#run-a-workflow
>
> A lot of this is very recent so if you run into any bugs or anything that
> is just not clear, let me know, the feedback is very helpful!
>
> Cheers,
> Clare
>
> On 8 March 2013 16:01, Rob Leclerc <robert.lecl...@gmail.com> wrote:
>
>> I had trouble running blend4j, so I tried to jump into python (a language
>> I have little experience with).
>>
>> I tried running the example run_import_workflow.py
>>
>> *% python run_imported_workflow.py 
>> http://localhost:80808c25bc83f6f9e4001dd21eb7b64f063f
>> *
>>
>> but I get an error:
>>
>> Initiating Galaxy connection
>> Importing workflow
>> Creating data library 'Imported data for API demo'
>>
>> Traceback (most recent call last):
>>   File "run_imported_workflow.py", line 53, in <module>
>>     library_dict = gi.libraries.create_library(library_name)
>>   File
>> "build/bdist.macosx-10.6-intel/egg/bioblend/galaxy/libraries/__init__.py",
>> line 27, in create_library
>>   File "build/bdist.macosx-10.6-intel/egg/bioblend/galaxy/client.py",
>> line 53, in _post
>>   File "build/bdist.macosx-10.6-intel/egg/bioblend/galaxy/__init__.py",
>> line 132, in make_post_request
>>   File
>> "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/requests-1.1.0-py2.7.egg/requests/models.py",
>> line 604, in json
>>     return json.loads(self.text or self.content)
>>   File
>> "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/simplejson-3.1.0-py2.7-macosx-10.6-intel.egg/simplejson/__init__.py",
>> line 454, in loads
>>     return _default_decoder.decode(s)
>>   File
>> "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/simplejson-3.1.0-py2.7-macosx-10.6-intel.egg/simplejson/decoder.py",
>> line 374, in decode
>>     obj, end = self.raw_decode(s)
>>   File
>> "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/simplejson-3.1.0-py2.7-macosx-10.6-intel.egg/simplejson/decoder.py",
>> line 393, in raw_decode
>>     return self.scan_once(s, idx=_w(s, idx).end())
>> simplejson.scanner.JSONDecodeError: Expecting value: line 1 column 1
>> (char 0)
>>
>>
>> Is there anything I am missing from the stock configuration which would
>> cause this not to run out of the box?
>>
>> Cheers,
>> Rob
>>
>> ___________________________________________________________
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>
>
>
> --
>
> Clare Sloggett
> Research Fellow / Bioinformatician
> Life Sciences Computation Centre
> Victorian Life Sciences Computation Initiative
> University of Melbourne, Parkville Campus
> 187 Grattan Street, Carlton, Melbourne
> Victoria 3010, Australia
> Ph: 03 903 53357          M: 0414 854 759
>



-- 

Clare Sloggett
Research Fellow / Bioinformatician
Life Sciences Computation Centre
Victorian Life Sciences Computation Initiative
University of Melbourne, Parkville Campus
187 Grattan Street, Carlton, Melbourne
Victoria 3010, Australia
Ph: 03 903 53357          M: 0414 854 759
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