Hello Enis,

I am trying to add PyCogent to the PYTHONPATH, but it seems the Fabric
run command does not recognize it. 
I tried:                 run("export
and then use cmd_install() to install Galaxy, but I keep getting the
message that PyCogent is not installed.

The normal strategy to use sys.path will not work because that will
adjust the PYTHONPATH on my local machine, not in the image if I am
Do you know a way to set the PYTHONPATH for Fabric' run() command?



On Thu, 2011-07-14 at 09:05 +0000, Enis Afgan wrote:
> 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.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

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

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