Oops sorry, meant to keep the list cc'd - resending. On 18 March 2013 16:18, Clare Sloggett <sloc@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-wo...

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.leclerc@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