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).
On Fri, Jul 15, 2011 at 12:19 PM, Mattias de Hollander <
> 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 : dependency_manager.find_dep('blast')
> > Out:
> > ('/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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