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.dehollander@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.dehollander@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.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
>         >
>         >
>
>
>
>         --
>
>         Bioinformatician
>         Netherlands Institute of Ecology (NIOO-KNAW)
>         Wageningen, the Netherlands
>
>
>


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