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.
Enis
On Wed, Jul 13, 2011 at 12:09 PM, Mattias de Hollander
<m.dehollander@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