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Some eggs are out of date, attempting to fetch...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/", line 37, in <module>
    c.resolve() # Only fetch eggs required by the config
  File "/Users/galaxy/galaxy-old3/lib/galaxy/eggs/", line 345,
in resolve
  File "/Users/galaxy/galaxy-old3/lib/galaxy/eggs/", line 195,
in resolve
    return self.version_conflict( e.args[0], e.args[1] )
  File "/Users/galaxy/galaxy-old3/lib/galaxy/eggs/", 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/", line 588, in
    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/ 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'
Override with: <forced-platform>
Completed packager is ''.  To
fetch eggs, please copy this file to a system with internet access and run

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

To search Galaxy mailing lists use the unified search at:

Reply via email to