Paul Tanger wrote:
I don't know if I did this correctly, but the output from python get_platforms.py is: macosx-10.5-i386-ucs2
Okay, it looks like EPD python is only compiled for one platform. To use this, you'll need to scramble your own versions of the eggs which use C code. Could you try scrambling pysam as instructed below and see what the results are? You will have to do this for each egg that can't be downloaded. --nate
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Some eggs are out of date, attempting to fetch...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 Some eggs are out of date, attempting to fetch...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/