Hi Mattias,
PyCogent is not currently being installed as part of mi-deployment, so the
method for installing it should be added (if you do so, please consider
issuing a pull request on bitbucket so it can be added to the project).

When it comes to composing $PYTHONPATH to include the reference to PyCogent
via Qiime's env.sh - this should be done as part of the Qiime installation
method in mi-deployment (something like export PYHTONPATH=<path where
PyCogent was installed>; export PATH=...).
Sourcing of the tool's env.sh script is prepended to the execution command
when running the tool so the appropriate environment settings will be loaded
before the tool is run.


On Wed, Jul 13, 2011 at 12:09 PM, Mattias de Hollander <
m.dehollan...@nioo.knaw.nl> wrote:

> 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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