Great! If you fork mi-deployment project on bitbucket and issue a pull
request, the new tool can be added to upstream (or send a patch via email
and I'll add it manually).

Thanks,
Enis

On Fri, Jul 15, 2011 at 2:03 PM, Mattias de Hollander <
m.dehollan...@nioo.knaw.nl> wrote:

> I just found out the former approach you mentioned. Its now installing
> perfectly. The latter approach won't work for a Qiime installation
> because its needs PyCogent on its path during the setup.py phase.
>
> Thanks for clarification.
> If I finished adding Qiime' dependencies I will put it on bitbucket.
>
> Greetz,
>
> Mattias
>
> On Fri, 2011-07-15 at 13:44 +0000, Enis Afgan wrote:
> > Each use of fabric's `run` method is independent so they cannot be
> > chained; you would either need to prepend the export command to the
> > command that depends on the fact PYTHONPATH is set (e.g., run("export
> > PYTHONPATH=...; <command that requires given PP>") or (better
> > approach) create an env.sh file in the Qiime's install dir so that it
> > includes the required 'export PYTHONPATH=...'. When Galaxy invokes
> > Qiime, it will automatically source that env.sh (assuming you have
> > config variable `tool_dependency_dir = /mnt/galaxyTools/tools` set in
> > Galaxy's universe_wsgi.ini).
> >
> > Enis
> >
> > On Fri, Jul 15, 2011 at 12:19 PM, Mattias de Hollander
> > <m.dehollan...@nioo.knaw.nl> wrote:
> >         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
> >
> PYTHONPATH=/mnt/galaxyTools/tools/PyCogent/1.5.1/lib/python2.6/site-packages/:$PYTHONPATH")
> >         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
> >         correct.
> >         Do you know a way to set the PYTHONPATH for Fabric' run()
> >         command?
> >
> >         Thanks,
> >
> >         Mattias
> >
> >
> >         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
> >         >
> >         >
> >
> >
> >
> >         --
> >
> >         Bioinformatician
> >         Netherlands Institute of Ecology (NIOO-KNAW)
> >         Wageningen, the Netherlands
> >
> >
> >
>
>
> --
> Bioinformatician
> Netherlands Institute of Ecology (NIOO-KNAW)
> Wageningen, the Netherlands
>
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