Error when starting up/running a local galaxy

Traceback (most recent call last):
  File "./scripts/", line 26, in <module>
  File "/usr/local/galaxy/lib/galaxy/util/pastescript/", line 1062, in run
    invoke(command, command_name, options, args[1:])
  File "/usr/local/galaxy/lib/galaxy/util/pastescript/", line 1068, in invoke
    exit_code =
  File "/usr/local/galaxy/lib/galaxy/util/pastescript/", line 224, in run
    result = self.command()
  File "/usr/local/galaxy/lib/galaxy/util/pastescript/", line 640, in command
    app = loadapp( app_spec, name=app_name, relative_to=base, global_conf=vars)
  File "/usr/local/galaxy/lib/galaxy/util/pastescript/", line 294, in loadapp
    return loadobj(APP, uri, name=name, **kw)
  File "/usr/local/galaxy/lib/galaxy/util/pastescript/", line 320, in loadobj
    return context.create()
  File "/usr/local/galaxy/lib/galaxy/util/pastescript/", line 761, in create
    return self.object_type.invoke(self)
  File "/usr/local/galaxy/lib/galaxy/util/pastescript/", line 276, in invoke
    filtered = context.next_context.create()
  File "/usr/local/galaxy/lib/galaxy/util/pastescript/", line 761, in create
    return self.object_type.invoke(self)
  File "/usr/local/galaxy/lib/galaxy/util/pastescript/", line 188, in invoke
    return fix_call(context.object, context.global_conf, **context.local_conf)
  File "/usr/local/galaxy/lib/galaxy/util/pastescript/", line 91, in fix_call
    val = callable(*args, **kw)
  File "/usr/local/galaxy/lib/galaxy/webapps/galaxy/", line 42, in app_factory
    return paste_app_factory( global_conf, **kwargs )
  File "/usr/local/galaxy/lib/galaxy/webapps/galaxy/", line 71, in paste_app_factory
    webapp.add_ui_controllers( 'galaxy.webapps.galaxy.controllers', app )
  File "/usr/local/galaxy/lib/galaxy/web/framework/", line 123, in add_ui_controllers
    module = import_module( module_name )
  File "/usr/lib/python2.7/importlib/", line 37, in import_module
  File "/usr/local/galaxy/lib/galaxy/webapps/galaxy/controllers/", line 10, in <module>
  File "/usr/local/galaxy/.venv/local/lib/python2.7/site-packages/", line 745, in require
    needed = self.resolve(parse_requirements(requirements))
  File "/usr/local/galaxy/.venv/local/lib/python2.7/site-packages/", line 639, in resolve
    raise DistributionNotFound(req)
pkg_resources.DistributionNotFound: simplejson
1 Like

Could you provide a bit more information, such as what Galaxy version you’re using, and the command(s) you’re executing to start Galaxy?


To run Galaxy I use sh
and how can i know the galaxy version ???


This seems to be a development version of release 17.09, which is out of support now. Any chance you can upgrade to 18.05 or 18.09?

1 Like

I am not sure what in that release (actually, you are running a dev version of 17.09) is requiring simplejson - can you run grep -rIi simplejson /usr/local/galaxy/lib ?

I would strongly encourage you to upgrade to the latest stable release, 18.09.

1 Like
/usr/local/galaxy/lib/galaxy/webapps/galaxy/controllers/ simplejson
/usr/local/galaxy/lib/galaxy/webapps/galaxy/controllers/        jsonjobs = simplejson.dumps( jobs )
/usr/local/galaxy/lib/galaxy/webapps/galaxy/controllers/        return trans.fill_template( '/admin/data_admin/ajax_status.mako', json=simplejson.dumps( jobs ) )
/usr/local/galaxy/lib/galaxy/webapps/demo_sequencer/framework/ "simplejson" )
/usr/local/galaxy/lib/galaxy/webapps/demo_sequencer/framework/ simplejson
/usr/local/galaxy/lib/galaxy/tools/genome_index/ simplejson
/usr/local/galaxy/lib/galaxy/tools/genome_index/                logloc = simplejson.load( fp )
/usr/local/galaxy/lib/galaxy/tools/genome_index/ simplejson
/usr/local/galaxy/lib/galaxy/tools/genome_index/        simplejson.dump( self.locations, self.outfile )

All these Python files (i.e. except for lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt) do not exist any more in Galaxy since at least 2015, which probably means your source code installation is quite messed-up.

1 Like

I made a galaxy update to version 19.05 and when I try to run it with the sh command it shows me this error.

Complete output from command python egg_info:

    running egg_info
    creating pip-egg-info/Beaker.egg-info
    writing requirements to pip-egg-info/Beaker.egg-info/requires.txt
    writing pip-egg-info/Beaker.egg-info/PKG-INFO
    writing top-level names to pip-egg-info/Beaker.egg-info/top_level.txt
    writing dependency_links to pip-egg-info/Beaker.egg-info/dependency_links.txt
    writing entry points to pip-egg-info/Beaker.egg-info/entry_points.txt
    Traceback (most recent call last):
      File "<string>", line 1, in <module>
      File "/tmp/pip-install-BQINXC/beaker/", line 112, in <module>
      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 "/usr/local/galaxy/.venv/local/lib/python2.7/site-packages/setuptools/command/", line 160, in run
        writer = ep.load(installer=installer)
      File "/usr/local/galaxy/.venv/local/lib/python2.7/site-packages/", line 2188, in load
        self.require(env, installer)
      File "/usr/local/galaxy/.venv/local/lib/python2.7/site-packages/", line 2202, in require
        items = working_set.resolve(reqs, env, installer)
      File "/usr/local/galaxy/.venv/local/lib/python2.7/site-packages/", line 644, in resolve
        raise VersionConflict(dist, req)
    pkg_resources.VersionConflict: (Paste 2.0.2 (/usr/local/galaxy/.venv/lib/python2.7/site-packages), Requirement.parse('Paste>=3.0'))
Command "python egg_info" failed with error code 1 in /tmp/pip-install-BQINXC/beaker/
1 Like

Hi, Avoid the release still in development. The current stable Galaxy release is now 19.01.

Hi! I just upgraded to 19.05 and ran into this exact same error. I would appreciate any suggestion on what I should try. Thank you!

1 Like

ping @nsoranzo @nate

I’d try to remove the Galaxy virtual environment (by default the .venv subdirectory of your Galaxy root folder) and try to start galaxy again.

1 Like