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Some eggs are out of date, attempting to fetch...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,
File "/Users/galaxy/galaxy-old3/lib/galaxy/eggs/__init__.py", line 195,
return self.version_conflict( e.args, e.args )
File "/Users/galaxy/galaxy-old3/lib/galaxy/eggs/__init__.py", line 226,
r = pkg_resources.working_set.resolve( ( dist.as_requirement(), ), env,
File "build/bdist.macosx-10.9-x86_64/egg/pkg_resources.py", line 588, in
The `plugin_env` should be an ``Environment`` instance that contains
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
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'
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
Plant and Wildlife Science Dept.
Brigham Young University
Provo, UT 84602