Hello,

I am trying to add tools (PyCogent, Qiime) to a Cloudman image using the
mi-deployment scripts. Qiime depends on PyCogent and it needs to be
accessible on the python path, otherwise I get an error:
PyCogent not installed but required. (Is it installed? Is it in the
current user's $PYTHONPATH or site-packages?)

Is there a way to add the paths in env.sh to the sys.path during
installation using tools_fabfile.py?
All the tools are in /mnt/galaxyTools/tools.
I tried the DependencyManager from galaxy but then I only receive the
path to the env.sh file:
In [43]: dependency_manager.find_dep('blast')
Out[43]: 
('/mnt/galaxyTools/tools/blast/2.2.25/env.sh',
 '/mnt/galaxyTools/tools/blast/2.2.25',
 '2.2.25')

Is there a smarter way to add files to the PYTHONPATH during the
execution of tools_fabfile.py?

Thanks,

Mattias

-- 
Bioinformatician
Netherlands Institute of Ecology (NIOO-KNAW)
Wageningen, the Netherlands

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