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