Question: Galaxy production server virtualenv
gravatar for jasperkoehorst
14 months ago by
jasperkoehorst10 wrote:

I might have found a solution:

I am trying to set up galaxy according to the production server page:

It immeadiatly goes wrong at the second step:

nate@weyerbacher% wget nate@weyerbacher% /usr/bin/python2.7 --no-site-packages galaxy_env

I get a long error list regarding the virtual env. But I also realised that this code tip is from 2011? Is this still correct?

New python executable in galaxy_env/bin/python2.7
Not overwriting existing python script galaxy_env/bin/python (you must use galaxy_env/bin/python2.7)
Installing setuptools............................................
  Complete output from command /home/galaxy/galaxy_env/bin/python2.7 -c "#!python
\"\"\"Bootstrap setuptoo...

" --always-copy -U setuptools:
Searching for setuptools
Best match: setuptools 36.5.0
Running setuptools-36.5.0/ -q bdist_egg --dist-dir /tmp/easy_install-0SwZTb/setuptools-36.5.0/egg-dist-tmp-gHdhr1
/usr/lib/python2.7/distutils/ UserWarning: Unknown distribution option: 'long_description_content_type'
/usr/lib/python2.7/distutils/ UserWarning: Unknown distribution option: 'src_root'
Traceback (most recent call last):
  File "<string>", line 278, in <module>
  File "<string>", line 213, in main
  File "/home/galaxy/setuptools-0.6c11-py2.7.egg/setuptools/command/", line 1712, in main
  File "/home/galaxy/setuptools-0.6c11-py2.7.egg/setuptools/command/", line 1700, in with_ei_usage
  File "/home/galaxy/setuptools-0.6c11-py2.7.egg/setuptools/command/", line 1716, in <lambda>
  File "/usr/lib/python2.7/distutils/", line 151, in setup
  File "/usr/lib/python2.7/distutils/", line 953, in run_commands
  File "/usr/lib/python2.7/distutils/", line 972, in run_command
  File "/home/galaxy/setuptools-0.6c11-py2.7.egg/setuptools/command/", line 211, in run
  File "/home/galaxy/setuptools-0.6c11-py2.7.egg/setuptools/command/", line 446, in easy_install
  File "/home/galaxy/setuptools-0.6c11-py2.7.egg/setuptools/command/", line 476, in install_item
  File "/home/galaxy/setuptools-0.6c11-py2.7.egg/setuptools/command/", line 655, in install_eggs
  File "/home/galaxy/setuptools-0.6c11-py2.7.egg/setuptools/command/", line 930, in build_and_install
  File "/home/galaxy/setuptools-0.6c11-py2.7.egg/setuptools/command/", line 919, in run_setup
  File "/home/galaxy/setuptools-0.6c11-py2.7.egg/setuptools/", line 62, in run_setup
  File "/home/galaxy/setuptools-0.6c11-py2.7.egg/setuptools/", line 105, in run
  File "/home/galaxy/setuptools-0.6c11-py2.7.egg/setuptools/", line 64, in <lambda>
  File "", line 188, in <module>
  File "/usr/lib/python2.7/distutils/", line 111, in setup
    _setup_distribution = dist = klass(attrs)
  File "/home/galaxy/setuptools-0.6c11-py2.7.egg/setuptools/", line 264, in __init__
  File "/usr/lib/python2.7/distutils/", line 287, in __init__
  File "/home/galaxy/setuptools-0.6c11-py2.7.egg/setuptools/", line 297, in finalize_options
  File "/home/galaxy/setuptools-0.6c11-py2.7.egg/", line 1959, in load
ImportError: <module 'setuptools.dist'="" from="" '="" home="" galaxy="" setuptools-0.6c11-py2.7.egg="" setuptools=""'=""> has no 'check_specifier' attribute
...Installing setuptools...done.
Traceback (most recent call last):
  File "", line 1649, in <module>
  File "", line 558, in main
  File "", line 654, in create_environment
    install_setuptools(py_executable, unzip=unzip_setuptools)
  File "", line 384, in install_setuptools
    _install_req(py_executable, unzip)
  File "", line 360, in _install_req
  File "", line 624, in call_subprocess
    % (cmd_desc, proc.returncode))
OSError: Command /home/galaxy/galaxy_env/bin/python2.7 -c "#!python
\"\"\"Bootstrap setuptoo...

" --always-copy -U setuptools failed with error code 1
production galaxy • 449 views
ADD COMMENTlink modified 14 months ago by Jennifer Hillman Jackson25k • written 14 months ago by jasperkoehorst10
gravatar for Jennifer Hillman Jackson
14 months ago by
United States
Jennifer Hillman Jackson25k wrote:


Thanks for the pull request fix and for posting back here! Please continue with the testing/troubleshooting at GitHub for any fine tuning (if needed).

For others that may encounter the same problem going forward: Please track status using the link at the top of the original post question above. The change was incorporated into the Galaxy master branch and will probably be included in the next stable release.

Thanks! Jen, Galaxy team

ADD COMMENTlink written 14 months ago by Jennifer Hillman Jackson25k
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