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
>
>
>