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
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 ___________________________________________________________ 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/ -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336.
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
___________________________________________________________ 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:
Assaf Gordon 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 ?
No, that's a mistake. I should have a fix committed shortly.
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
___________________________________________________________ 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:
___________________________________________________________ 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:
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
___________________________________________________________ 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:
___________________________________________________________ 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:
participants (4)
-
Assaf Gordon -
Kanwei Li -
Nate Coraor -
WATSON Mick