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Some eggs are out of date, attempting to fetch...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 - 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 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/