Re: [galaxy-dev] Installing tools with dependencies using mi-deployment scripts

15 Jul 2011

      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