That worked, for everything but pysam.  I also tried to install it 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Some eggs are out of date, attempting to fetch...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.

On Mon, Aug 29, 2011 at 10:51 AM, Nate Coraor <n...@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 Some eggs are out of date, attempting to fetch...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 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.
>
> 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 <n...@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.tan...@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 <n...@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 <n...@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.tan...@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.tan...@colostate.edu
http://bioenergy-igert.colostate.edu/
___________________________________________________________
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