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 <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 ?
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",
WATSON Mick wrote, On 04/28/2011 04:11 PM: 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
File "/home/gordon/temp/galaxy_hidden_dataset_test/lib/galaxy/visualization/tracks/data_providers.py",
get_data_provider 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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