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