Getting somewhere, but it looks like it can't find numpy 1.6? error returned is: pkg_resources is: <module 'pkg_resources' from '/Users/paultanger/galaxy-dist/lib/pkg_resources.py'> Some eggs are out of date, attempting to fetch... pkg_resources is: <module 'pkg_resources' from '/Users/paultanger/galaxy-dist/lib/pkg_resources.pyc'> Warning: MarkupSafe (a dependent egg of Mako) cannot be fetched Fetched http://eggs.g2.bx.psu.edu/Babel/Babel-0.9.4-py2.6.egg Fetched http://eggs.g2.bx.psu.edu/Whoosh/Whoosh-0.3.18-py2.6.egg Fetched http://eggs.g2.bx.psu.edu/Tempita/Tempita-0.1-py2.6.egg Fetched http://eggs.g2.bx.psu.edu/lrucache/lrucache-0.2-py2.6.egg Fetched http://eggs.g2.bx.psu.edu/NoseHTML/NoseHTML-0.4.1-py2.6.egg Fetched http://eggs.g2.bx.psu.edu/pexpect/pexpect-2.4-py2.6.egg Fetched http://eggs.g2.bx.psu.edu/amqplib/amqplib-0.6.1-py2.6.egg Fetched http://eggs.g2.bx.psu.edu/PasteDeploy/PasteDeploy-1.3.3-py2.6.egg Fetched http://eggs.g2.bx.psu.edu/WebHelpers/WebHelpers-0.2-py2.6.egg Fetched http://eggs.g2.bx.psu.edu/docutils/docutils-0.7-py2.6.egg Traceback (most recent call last): File "./scripts/fetch_eggs.py", line 32, in <module> c.resolve() # Only fetch eggs required by the config File "/Users/paultanger/galaxy-dist/lib/galaxy/eggs/__init__.py", line 347, in resolve egg.resolve() File "/Users/paultanger/galaxy-dist/lib/galaxy/eggs/__init__.py", line 197, in resolve return self.version_conflict( e.args[0], e.args[1] ) File "/Users/paultanger/galaxy-dist/lib/galaxy/eggs/__init__.py", line 228, in version_conflict r = pkg_resources.working_set.resolve( ( dist.as_requirement(), ), env, egg.fetch ) File "/Users/paultanger/galaxy-dist/lib/pkg_resources.py", line 565, in resolve raise DistributionNotFound(req) # XXX put more info here pkg_resources.DistributionNotFound: numpy==1.6.0 Fetch failed. On Mon, Aug 29, 2011 at 10:18 AM, Nate Coraor <nate@bx.psu.edu> wrote:
Paul Tanger wrote:
sys path is:
['/Users/paultanger/galaxy-dist/scripts', '/Users/paultanger/python/scripts', '/Library/Frameworks/Python.framework/Versions/6.1/lib/python26.zip', '/Library/Frameworks/Python.framework/Versions/6.1/lib/python2.6',
'/Library/Frameworks/Python.framework/Versions/6.1/lib/python2.6/plat-darwin',
'/Library/Frameworks/Python.framework/Versions/6.1/lib/python2.6/plat-mac',
'/Library/Frameworks/Python.framework/Versions/6.1/lib/python2.6/plat-mac/lib-scriptpackages',
'/Library/Frameworks/Python.framework/Versions/6.1/lib/python2.6/lib-tk',
'/Library/Frameworks/Python.framework/Versions/6.1/lib/python2.6/lib-old',
'/Library/Frameworks/Python.framework/Versions/6.1/lib/python2.6/lib-dynload',
'/Library/Frameworks/Python.framework/Versions/6.1/lib/python2.6/site-packages',
'/Library/Frameworks/Python.framework/Versions/6.1/lib/python2.6/site-packages/PIL',
'/Users/paultanger/galaxy-dist/lib']
Hi Paul,
If you replace:
lib = os.path.abspath( os.path.join( os.path.dirname( __file__ ), "..", "lib" ) ) sys.path.append( lib )
With:
lib = os.path.abspath( os.path.join( os.path.dirname( __file__ ), "..", "lib" ) ) sys.path.insert( 0, lib )
In scripts/check_eggs.py and scripts/fetch_eggs.py, does this have an effect?
--nate
pkg_resources is: <module 'pkg_resources' from
'/Library/Frameworks/Python.framework/Versions/6.1/lib/python2.6/site-packages/pkg_resources.py'>
On Mon, Aug 29, 2011 at 8:17 AM, Paul Tanger <paul.tanger@colostate.edu wrote:
It is free for academic use. I'll try what you suggested below -
On Mon, Aug 29, 2011 at 7:59 AM, Nate Coraor <nate@bx.psu.edu> wrote:
Paul Tanger wrote:
Yes it works with the default python install. Any way I can get it working with EPD python?
I've never worked with EPD and since it's not free it's unlikely we
can
do much debugging on it here. It would appear that they bundle a version of pkg_resources which changes the DistributionNotFound class, but it's hard to know exactly what's going on here.
One thing that might shed a bit of light on it would be to print sys.path and pkg_resources at the top of:
galaxy-dist/lib/galaxy/eggs/__init__.py
After the import of pkg_resources and see which version it's using.
--nate
On Fri, Aug 26, 2011 at 12:43 PM, Nate Coraor <nate@bx.psu.edu>
wrote:
Paul Tanger wrote: > Has anyone gotten galaxy installed on a mac 10.5 with EPD
python > 2.6 (EPD version 6.1-1)? I get this error which I suspect is related to the > fact that I have EPD python, not the generic python that was preinstalled? > Any ideas? > > Thanks! > > Some eggs are out of date, attempting to fetch... > Traceback (most recent call last): > File "./scripts/fetch_eggs.py", line 30, in <module> > c.resolve() # Only fetch eggs required by the config > File "/Users/paultanger/galaxy-dist/lib/galaxy/eggs/__init__.py",
> 345, in resolve > egg.resolve() > File "/Users/paultanger/galaxy-dist/lib/galaxy/eggs/__init__.py",
(enthought) line line
> 184, in resolve > if e.args[0].project_name != self.distribution.project_name: > AttributeError: 'str' object has no attribute 'project_name' > Fetch failed.
Hi Paul,
Can you give it a try with the system Python and see if you get
thanks! the
same
result? All you need to do is put:
/System/Library/Frameworks/Python.framework/Versions/2.6/bin
At the head of your $PATH.
Thanks, --nate
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-- _____________________________________ Paul Tanger NSF IGERT Bioenergy Fellow Bioagricultural Sciences and Pest Management Colorado State University 1177 Campus Delivery Fort Collins, CO 80523-1177 paul.tanger@colostate.edu http://bioenergy-igert.colostate.edu/