Hi Galaxy developers,

There is a version of pkg_resources.py in /lib, which seems to be from some 
specific version of setuptools.

We had a problem scrambling eggs in Galaxy, as e.g. follows:

fetch_one(): Trying to fetch:
  http://eggs.galaxyproject.org/Mako/Mako-0.4.1.tar.gz
fetch_one(): Fetched to:
  
/software/elixir/hb-nels/galaxy-dist/scripts/scramble/archives/Mako-0.4.1.tar.gz
unpack_source(): Unpacked to:
  /software/elixir/hb-nels/galaxy-dist/scripts/scramble/build/py2.7/Mako
copy_build_script(): Using build script 
/software/elixir/hb-nels/galaxy-dist/scripts/scramble/scripts/generic.py
run_scramble_script(): Beginning build
run_scramble_script(): Executing in 
/software/elixir/hb-nels/galaxy-dist/scripts/scramble/build/py2.7/Mako:
  /software/VERSIONS/python2-2.7.6/bin/python scramble.py
/software/VERSIONS/python2-2.7.6/lib/python2.7/distutils/dist.py:267: 
UserWarning: Unknown distribution option: 'entry_points'
  warnings.warn(msg)
/software/VERSIONS/python2-2.7.6/lib/python2.7/distutils/dist.py:267: 
UserWarning: Unknown distribution option: 'extras_require'
  warnings.warn(msg)
/software/VERSIONS/python2-2.7.6/lib/python2.7/distutils/dist.py:267: 
UserWarning: Unknown distribution option: 'install_requires'
  warnings.warn(msg)
/software/VERSIONS/python2-2.7.6/lib/python2.7/distutils/dist.py:267: 
UserWarning: Unknown distribution option: 'zip_safe'
  warnings.warn(msg)
/software/VERSIONS/python2-2.7.6/lib/python2.7/distutils/dist.py:267: 
UserWarning: Unknown distribution option: 'test_suite'
  warnings.warn(msg)
/software/VERSIONS/python2-2.7.6/lib/python2.7/distutils/dist.py:267: 
UserWarning: Unknown distribution option: 'tests_require'
  warnings.warn(msg)
usage: scramble.py [global_opts] cmd1 [cmd1_opts] [cmd2 [cmd2_opts] ...]
   or: scramble.py --help [cmd1 cmd2 ...]
   or: scramble.py --help-commands
   or: scramble.py cmd --help

After much searching we found that the error was caused by some form of 
incompatibility with the pkg_resources.py in Galaxy and the version of 
setuptools installed on our server (3.8). Removing the pkg_resouces.py in 
galaxy solved the issue.

Is there a good reason for the pkg_resources to be distributed with Galaxy or 
should this file perhaps be removed?

Does Galaxy require a specific version of setuptools to be installed?

Kind regards,
Sveinung Gundersen

--
Sveinung Gundersen, PhD

Senior engineer, ELIXIR.NO / The Genomic HyperBrowser team
Department of Informatics, University of Oslo, Norway

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