I've just tried an initial installation of Galaxy (galaxy_dist) on a Fedora 13 machine. When I try to run the setup.sh script I get the error below:
Creating tool-data/shared/jars Traceback (most recent call last): File "./scripts/fetch_eggs.py", line 31, in <module> c.resolve() # Only fetch eggs required by the config File "/data/private/galaxy/galaxy_dist/lib/galaxy/eggs/__init__.py", line 284, in resolve egg.resolve() File "/data/private/galaxy/galaxy_dist/lib/galaxy/eggs/__init__.py", line 172, in resolve r = pkg_resources.working_set.resolve( ( self.distribution.as_requirement(), ), env, self.fetch ) File "/data/private/galaxy/galaxy_dist/lib/pkg_resources.py", line 565, in res olve raise DistributionNotFound(req) # XXX put more info here pkg_resources.DistributionNotFound: simplejson==1.5
Fedora 13 comes with simplejson v2.1.1. Is there really a strict requirement on v1.5 or should the test be >=1.5? Is there a way to parallel install different versions of this package if 1.5 is strictly required?
Thanks
Simon.
simon andrews (BI) wrote:
I've just tried an initial installation of Galaxy (galaxy_dist) on a Fedora 13 machine. When I try to run the setup.sh script I get the error below:
Creating tool-data/shared/jars Traceback (most recent call last): File "./scripts/fetch_eggs.py", line 31, in <module> c.resolve() # Only fetch eggs required by the config File "/data/private/galaxy/galaxy_dist/lib/galaxy/eggs/__init__.py", line 284, in resolve egg.resolve() File "/data/private/galaxy/galaxy_dist/lib/galaxy/eggs/__init__.py", line 172, in resolve r = pkg_resources.working_set.resolve( ( self.distribution.as_requirement(), ), env, self.fetch ) File "/data/private/galaxy/galaxy_dist/lib/pkg_resources.py", line 565, in res olve raise DistributionNotFound(req) # XXX put more info here pkg_resources.DistributionNotFound: simplejson==1.5
Fedora 13 comes with simplejson v2.1.1. Is there really a strict requirement on v1.5 or should the test be >=1.5? Is there a way to parallel install different versions of this package if 1.5 is strictly required?
Hi Simon,
Galaxy does use old versions of some modules - due to the large number of dependencies, we don't always have the time to test new releases, and new versions can break Galaxy.
However, we pre-build most of our dependencies and Galaxy automatically downloads them. You may want to try the following:
python scripts/fetch_eggs.py
If all of your dependencies are up to date, you may have encountered a version conflict which we haven't correctly handled, which you can resolve by setting up a virtualenv, which is explained here:
http://usegalaxy.org/production
--nate
Thanks
Simon.
galaxy-dev mailing list galaxy-dev@lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-dev
On 29 Jul 2010, at 14:39, Nate Coraor wrote:
simon andrews (BI) wrote:
I've just tried an initial installation of Galaxy (galaxy_dist) on a Fedora 13 machine. When I try to run the setup.sh script I get the error below:
pkg_resources.DistributionNotFound: simplejson==1.5
Fedora 13 comes with simplejson v2.1.1. Is there really a strict requirement on v1.5 or should the test be >=1.5? Is there a way to parallel install different versions of this package if 1.5 is strictly required?
Hi Simon,
Galaxy does use old versions of some modules - due to the large number of dependencies, we don't always have the time to test new releases, and new versions can break Galaxy.
However, we pre-build most of our dependencies and Galaxy automatically downloads them. You may want to try the following:
python scripts/fetch_eggs.py
After more investigation it turns out the reasons for the failures wasn't the incompatible versions (as you said the fetch_eggs.py script should have pulled down the correct version). The reason this failed on our system was that python wasn't reading our proxy information correctly from the environment. I'd set the http_proxy variable, but python requires that the value includes the protocol information as well as the server and port. Since it couldn't access the download site it was falling back on the system installed version and was therefore throwing the version errors I saw.
After fixing the proxy information galaxy downloaded the correct versions of the various eggs and all is well.
Cheers
Simon.
simon andrews (BI) wrote:
After more investigation it turns out the reasons for the failures wasn't the incompatible versions (as you said the fetch_eggs.py script should have pulled down the correct version). The reason this failed on our system was that python wasn't reading our proxy information correctly from the environment. I'd set the http_proxy variable, but python requires that the value includes the protocol information as well as the server and port. Since it couldn't access the download site it was falling back on the system installed version and was therefore throwing the version errors I saw.
After fixing the proxy information galaxy downloaded the correct versions of the various eggs and all is well.
Excellent, and thanks for sharing your solution.
--nate
Cheers
Simon.
galaxy-dev mailing list galaxy-dev@lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-dev
galaxy-dev@lists.galaxyproject.org
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Nate Coraor -
simon andrews (BI)