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Some eggs are out of date, attempting to fetch...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 Some eggs are out of date, attempting to fetch...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

--
_____________________________________
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/