On Thu, Apr 28, 2011 at 4:28 PM, Assaf Gordon <gordon@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-bounces@lists.bx.psu.edu [galaxy-dev-bounces@lists.bx.psu.edu] On Behalf Of Assaf Gordon [gordon@cshl.edu]
> Sent: 28 April 2011 20:52
> To: galaxy-dev@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
>
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