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
___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client. To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
http://lists.bx.psu.edu/
