For various reasons, I installed a Homebrew of python instead of the system version on OSX 10.9.2.

Now, when galaxy initializes, it isn't looking in the right location for eggs (or they aren't placed in the right spot on my system). I was able to manually install several of the eggs and the galaxy startup would move to the next egg until here.

Some eggs are out of date, attempting to fetch...
Warning: MarkupSafe (a dependent egg of WebHelpers) cannot be fetched
Traceback (most recent call last):
  File "./scripts/fetch_eggs.py", line 37, in <module>
    c.resolve() # Only fetch eggs required by the config
  File "/Users/galaxy/galaxy-old3/lib/galaxy/eggs/__init__.py", line 345, in resolve
    egg.resolve()
  File "/Users/galaxy/galaxy-old3/lib/galaxy/eggs/__init__.py", line 195, in resolve
    return self.version_conflict( e.args[0], e.args[1] )
  File "/Users/galaxy/galaxy-old3/lib/galaxy/eggs/__init__.py", line 226, in version_conflict
    r = pkg_resources.working_set.resolve( ( dist.as_requirement(), ), env, egg.fetch )
  File "build/bdist.macosx-10.9-x86_64/egg/pkg_resources.py", line 588, in resolve
    The `plugin_env` should be an ``Environment`` instance that contains
pkg_resources.DistributionNotFound: numpy==1.6.0
Fetch failed.

I know numpy, WebHelpers, MarkupSafe are installed and they are current (maybe too current?) ... what would be a good way to resolve the conflict?

The manual download below fails on a dozen packages or so.

sudo python ./scripts/make_egg_packager.py py2.7-macosx-10.9-x86_64-ucs2
Using Python interpreter at /usr/local/Cellar/python/2.7.6/Frameworks/Python.framework/Versions/2.7/Resources/Python.app/Contents/MacOS/Python, Version 2.7.6 (default, Mar 24 2014, 14:39:40)
[GCC 4.2.1 Compatible Apple LLVM 5.1 (clang-503.0.38)]
This platform is 'py2.7-macosx-10.9-x86_64-ucs2'
Override with:
  make_egg_packager.py <forced-platform>
Completed packager is 'egg_packager-py2.7-macosx-10.9-x86_64-ucs2.py'.  To
fetch eggs, please copy this file to a system with internet access and run
with:
  python egg_packager-py2.7-macosx-10.9-x86_64-ucs2.py

--
Joshua Udall
Assistant Professor
295 WIDB
Plant and Wildlife Science Dept.
Brigham Young University
Provo, UT 84602
801-422-9307
Fax: 801-422-0008
USA

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