Hi Assaf,

Nate has just committed a fix so this shouldn't be required now. Thanks for
the report!

K

On Thu, Apr 28, 2011 at 4:28 PM, Assaf Gordon <gor...@cshl.edu> wrote:

> I'll rephrase my question:
> Is "cython" going to be a standard requirement for Galaxy (and needs to be
> manually installed on our production servers), or is this just a temporary
> thing, or is it going to be an automatic egg thing ?
>
> WATSON Mick wrote, On 04/28/2011 04:11 PM:
> > Looks like it :)
> >
> > http://cython.org/#download
> > ________________________________________
> > From: galaxy-dev-boun...@lists.bx.psu.edu [
> galaxy-dev-boun...@lists.bx.psu.edu] On Behalf Of Assaf Gordon [
> gor...@cshl.edu]
> > Sent: 28 April 2011 20:52
> > To: galaxy-...@bx.psu.edu
> > Subject: [galaxy-dev] problem running latest "galaxy-central"
> >
> > Question:
> >
> > The recent galaxy-central revision ( 2b057869b72f ) doesn't work on my
> computer, saying "DistributionNotFound: cython>=0.12.1".
> >
> > Example:
> > $ hg clone 
> > http://bitbucket.org/galaxy/galaxy-central/galaxy_hidden_dataset_test
> > $ cd galaxy_hidden_dataset_test
> > $ hg id
> > 2b057869b72f tip
> > $ sh run.sh
> > ...
> > ...
> > ...
> > Traceback (most recent call last):
> >   File
> "/home/gordon/temp/galaxy_hidden_dataset_test/lib/galaxy/web/buildapp.py",
> line 81, in app_factory
> >     from galaxy.app import UniverseApplication
> >   File "/home/gordon/temp/galaxy_hidden_dataset_test/lib/galaxy/app.py",
> line 11, in <module>
> >     from galaxy.tools.imp_exp import load_history_imp_exp_tools
> >   File
> "/home/gordon/temp/galaxy_hidden_dataset_test/lib/galaxy/tools/imp_exp/__init__.py",
> line 6, in <module>
> >     from galaxy.web.base.controller import UsesHistory
> >   File
> "/home/gordon/temp/galaxy_hidden_dataset_test/lib/galaxy/web/base/controller.py",
> line 12, in <module>
> >     from galaxy.visualization.tracks.data_providers import
> get_data_provider
> >   File
> "/home/gordon/temp/galaxy_hidden_dataset_test/lib/galaxy/visualization/tracks/data_providers.py",
> line 11, in <module>
> >     pkg_resources.require( "pysam" )
> >   File
> "/home/gordon/temp/galaxy_hidden_dataset_test/lib/galaxy/eggs/__init__.py",
> line 404, in require
> >     return c[req.project_name].require()
> >   File
> "/home/gordon/temp/galaxy_hidden_dataset_test/lib/galaxy/eggs/__init__.py",
> line 237, in require
> >     dists = self.resolve()
> >   File
> "/home/gordon/temp/galaxy_hidden_dataset_test/lib/galaxy/eggs/__init__.py",
> line 195, in resolve
> >     return self.version_conflict( e.args[0], e.args[1] )
> >   File
> "/home/gordon/temp/galaxy_hidden_dataset_test/lib/galaxy/eggs/__init__.py",
> line 226, in version_conflict
> >     r = pkg_resources.working_set.resolve( ( dist.as_requirement(), ),
> env, egg.fetch )
> >   File
> "/home/gordon/temp/galaxy_hidden_dataset_test/lib/pkg_resources.py", line
> 565, in resolve
> >     raise DistributionNotFound(req)  # XXX put more info here
> > DistributionNotFound: cython>=0.12.1
> >
> > =============
> >
> > I'm running debian/stable, with Python 2.6.6 (r266:84292, Dec 26 2010,
> 22:31:48)
> >
> > Do I need to install something (cython) ?
> >
> > -gordon
> >
> > ___________________________________________________________
> > 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/
> >
>
> ___________________________________________________________
> 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/
>
___________________________________________________________
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/

Reply via email to