Galaxy cannot use MacPorts Python

[Rodolfo Aramayo]

People,

This relates to the installation of Galaxy (http://main.g2.bx.psu.edu/) on a Mac

I am observing an error when I try to use the MacPorts installation of
Python to run Galaxy, but not when I use the Apple installation of
Python to run Galaxy

Disclaimer:
I am not sure this relates to, or can be resolved by the people of
MacPorts But I need to ask anyways

According to the Galaxy developers instructions, to have a local
installation of Galaxy one must:

A. Tell Galaxy where Python lives by creating a new directory at the
front of ##$PATH## and creating a symbolic link to python in that
directory in your home directory:

1 % mkdir ~/galaxy-python
2 % ln -s /path/to/python2.5 ~/galaxy-python/python
3 % export PATH=~/galaxy-python:$PATH

B. Get the latest version from the repository:

4 % hg clone https://bitbucket.org/galaxy/galaxy-dist/

C. Start Galaxy up

5 % sh run.sh

Now if I do that pointing to the Apple Python I get no errors and the
Galaxy server starts normally.
(i.e., using ' python -> /usr/bin/python' as a link inside the
'~/galaxy-python' directory)

Python is capable of initializing paths:
==========
python path is:
/Users/babieca/galaxy-central/eggs/numpy-1.6.0-py2.6-macosx-10.6-universal-ucs2.egg,
/Users/babieca/galaxy-central/eggs/pysam-0.4.2_kanwei_b10f6e722e9a-py2.6-macosx-10.6-universal-ucs2.egg,
/Users/babieca/galaxy-central/eggs/Whoosh-0.3.18-py2.6.egg,
/Users/babieca/galaxy-central/eggs/pycrypto-2.0.1-py2.6-macosx-10.6-universal-ucs2.egg,
/Users/babieca/galaxy-central/eggs/python_lzo-1.08_2.03_static-py2.6-macosx-10.6-universal-ucs2.egg,
/Users/babieca/galaxy-central/eggs/bx_python-0.7.0_494c2d1d68b3_rebuild1-py2.6-macosx-10.6-universal-ucs2.egg,
/Users/babieca/galaxy-central/eggs/amqplib-0.6.1-py2.6.egg,
/Users/babieca/galaxy-central/eggs/pexpect-2.4-py2.6.egg,
/Users/babieca/galaxy-central/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg,
/Users/babieca/galaxy-central/eggs/Babel-0.9.4-py2.6.egg,
/Users/babieca/galaxy-central/eggs/MarkupSafe-0.12-py2.6-macosx-10.6-universal-ucs2.egg,
/Users/babieca/galaxy-central/eggs/Mako-0.4.1-py2.6.egg,
/Users/babieca/galaxy-central/eggs/WebHelpers-0.2-py2.6.egg,
/Users/babieca/galaxy-central/eggs/simplejson-2.1.1-py2.6-macosx-10.6-universal-ucs2.egg,
/Users/babieca/galaxy-central/eggs/wchartype-0.1-py2.6.egg,
/Users/babieca/galaxy-central/eggs/elementtree-1.2.6_20050316-py2.6.egg,
/Users/babieca/galaxy-central/eggs/docutils-0.7-py2.6.egg,
/Users/babieca/galaxy-central/eggs/WebOb-0.8.5-py2.6.egg,
/Users/babieca/galaxy-central/eggs/Routes-1.12.3-py2.6.egg,
/Users/babieca/galaxy-central/eggs/Cheetah-2.2.2-py2.6-macosx-10.6-universal-ucs2.egg,
/Users/babieca/galaxy-central/eggs/PasteDeploy-1.3.3-py2.6.egg,
/Users/babieca/galaxy-central/eggs/PasteScript-1.7.3-py2.6.egg,
/Users/babieca/galaxy-central/eggs/Paste-1.6-py2.6.egg,
/Users/babieca/galaxy-central/lib, /usr/lib/python26.zip,
/usr/lib/python2.6, /usr/lib/python2.6/plat-darwin,
/usr/lib/python2.6/plat-mac,
/usr/lib/python2.6/plat-mac/lib-scriptpackages,
/usr/Extras/lib/python, /usr/lib/python2.6/lib-tk,
/usr/lib/python2.6/lib-old, /usr/lib/python2.6/lib-dynload,
/Library/Python/2.6/site-packages/Numeric,
/Library/Python/2.6/site-packages/PIL,
/Library/Python/2.6/site-packages/setuptools-0.6c11-py2.6.egg-info,
/opt/local/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages
==========

If however I point to the MacPorts Python I get the following error:
(i.e., using ' python -> /opt/local/bin/python' as a link inside the
'~/galaxy-python' directory)

==========
Some eggs are out of date, attempting to fetch...
Warning: MarkupSafe (a dependent egg of Mako) cannot be fetched
Warning: simplejson (a dependent egg of WebHelpers) cannot be fetched
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/babieca/galaxy-central/lib/galaxy/eggs/__init__.py",
line 345, in resolve
    egg.resolve()
  File "/Users/babieca/galaxy-central/lib/galaxy/eggs/__init__.py",
line 195, in resolve
    return self.version_conflict( e.args[0], e.args[1] )
  File "/Users/babieca/galaxy-central/lib/galaxy/eggs/__init__.py",
line 226, in version_conflict
    r = pkg_resources.working_set.resolve( ( dist.as_requirement(), ),
env, egg.fetch )
  File "/opt/local/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/pkg_resources.py",
line 584, in resolve
    raise DistributionNotFound(req)
pkg_resources.DistributionNotFound: numpy==1.6.0
Fetch failed.
==========

Why would the fetch failed??
Why Galaxy be unable to use MacPorts Python to fetch these eggs?
Is this a bug of MacPorts Python or inability of Galaxy code to
recognize a different installation of Python?

Given my ignorance I need to ask...\

Any Ideas would be really appreciated

Thanks

--R