I don't know if I did this correctly, but the output from python get_platforms.py is: macosx-10.5-i386-ucs2 On Mon, Aug 29, 2011 at 12:13 PM, Nate Coraor <nate@bx.psu.edu> wrote:
That worked, for everything but pysam. I also tried to install it
Paul Tanger wrote: directly:
pysam 0.4.2 couldn't be downloaded automatically. You can try building it by hand with: python scripts/scramble.py -e pysam
Some eggs are out of date, attempting to fetch...
pkg_resources is: <module 'pkg_resources' from '/Users/paultanger/galaxy-dist/lib/pkg_resources.pyc'> pysam 0.4.2 couldn't be downloaded automatically. You can try building it by hand with: python scripts/scramble.py -e pysam Fetch failed.
What platform do you get from:
python ./scripts/get_platforms.py
? Note that this needs to have the path changed from append to insert as in the previous scripts.
Thanks, --nate
On Mon, Aug 29, 2011 at 10:51 AM, Nate Coraor <nate@bx.psu.edu> wrote:
Paul Tanger wrote:
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 Some eggs are out of date, attempting to fetch...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
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",
347, in resolve egg.resolve() File "/Users/paultanger/galaxy-dist/lib/galaxy/eggs/__init__.py",
197, in resolve return self.version_conflict( e.args[0], e.args[1] ) File "/Users/paultanger/galaxy-dist/lib/galaxy/eggs/__init__.py",
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.
It could be a conflict with the existing version, try:
python -ES ./scripts/fetch_eggs.py
--nate
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
thanks!
> > > 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
http://eggs.g2.bx.psu.edu/WebHelpers/WebHelpers-0.2-py2.6.egg line line line - 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 >> (enthought) >> > > 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", >> line >> > > > 345, in resolve >> > > > egg.resolve() >> > > > File "/Users/paultanger/galaxy-dist/lib/galaxy/eggs/__init__.py", >> 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 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 >> > > >> > > >
>> > > > 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/ >> > > >> > > >> > > >
-- _____________________________________ 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/
-- _____________________________________ 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/
-- _____________________________________ 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/