BioBlend is a Python library for interacting with CloudMan and Galaxy's API.

BioBlend is supported and tested on:

• Python 2.6 and 2.7 (Python 3.3 and 3.4 have been added in the unreleased master branch)
• Galaxy release_14.02 and later.

Full docs are available at http://bioblend.readthedocs.org with a quick library overview also available in ABOUT.rst.

Modifications to Bioblend to make it work with Galaxy in the CCC.

All development will be done using Python 2.7 (should work with 2.6, but no guarantees)

Sample scripts are in the directory sample_scripts - you may have to tweak them to work with your Galaxy instance. Most of them expect a Python file called galaxy_key.py with the following two lines to be present in your Python search path (use PYTHONPATH environment variable).

galaxy_key='<Galaxy_API_key>';

galaxy_host='http://\<galaxy_host>:<port>';

Note that the galaxy_key is a secret key and should NOT be shared with other users. Make sure your galaxy_key.py file cannot be read by other users.

Make sure Python imports this Bioblend and not the system default. Some Python installations have their own versions installed and simply setting PYTHONPATH will not override the search path. Instead, add something like this in your galaxy_key.py file:

import sys;

sys.path = [ "<path_to_this_bioblend's_parent_directory>" ] + sys.path;