Error when starting up/running a local galaxy

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1 
Traceback (most recent call last):
  File "./scripts/paster.py", line 26, in <module>
    serve.run()
  File "/usr/local/galaxy/lib/galaxy/util/pastescript/serve.py", line 1062, in run
    invoke(command, command_name, options, args[1:])
  File "/usr/local/galaxy/lib/galaxy/util/pastescript/serve.py", line 1068, in invoke
    exit_code = runner.run(args)
  File "/usr/local/galaxy/lib/galaxy/util/pastescript/serve.py", line 224, in run
    result = self.command()
  File "/usr/local/galaxy/lib/galaxy/util/pastescript/serve.py", 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/loadwsgi.py", line 294, in loadapp
    return loadobj(APP, uri, name=name, **kw)
  File "/usr/local/galaxy/lib/galaxy/util/pastescript/loadwsgi.py", line 320, in loadobj
    return context.create()
  File "/usr/local/galaxy/lib/galaxy/util/pastescript/loadwsgi.py", line 761, in create
    return self.object_type.invoke(self)
  File "/usr/local/galaxy/lib/galaxy/util/pastescript/loadwsgi.py", line 276, in invoke
    filtered = context.next_context.create()
  File "/usr/local/galaxy/lib/galaxy/util/pastescript/loadwsgi.py", line 761, in create
    return self.object_type.invoke(self)
  File "/usr/local/galaxy/lib/galaxy/util/pastescript/loadwsgi.py", line 188, in invoke
    return fix_call(context.object, context.global_conf, **context.local_conf)
  File "/usr/local/galaxy/lib/galaxy/util/pastescript/loadwsgi.py", line 91, in fix_call
    val = callable(*args, **kw)
  File "/usr/local/galaxy/lib/galaxy/webapps/galaxy/buildapp.py", line 42, in app_factory
    return paste_app_factory( global_conf, **kwargs )
  File "/usr/local/galaxy/lib/galaxy/webapps/galaxy/buildapp.py", line 71, in paste_app_factory
    webapp.add_ui_controllers( 'galaxy.webapps.galaxy.controllers', app )
  File "/usr/local/galaxy/lib/galaxy/web/framework/webapp.py", line 123, in add_ui_controllers
    module = import_module( module_name )
  File "/usr/lib/python2.7/importlib/__init__.py", line 37, in import_module
    __import__(name)
  File "/usr/local/galaxy/lib/galaxy/webapps/galaxy/controllers/data_admin.py", line 10, in <module>
    pkg_resources.require("simplejson")
  File "/usr/local/galaxy/.venv/local/lib/python2.7/site-packages/pkg_resources.py", line 745, in require
    needed = self.resolve(parse_requirements(requirements))
  File "/usr/local/galaxy/.venv/local/lib/python2.7/site-packages/pkg_resources.py", line 639, in resolve
    raise DistributionNotFound(req)
pkg_resources.DistributionNotFound: simplejson
1 Like
2

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?

2 Likes
3

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

4

VERSION_MAJOR = “17.09”
VERSION_MINOR = “dev”
VERSION = VERSION_MAJOR + (’.’ + VERSION_MINOR if VERSION_MINOR else ‘’)

5

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
6

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
7 
/usr/local/galaxy/lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt:simplejson==3.16.0
/usr/local/galaxy/lib/galaxy/webapps/galaxy/controllers/data_admin.py:pkg_resources.require("simplejson")
/usr/local/galaxy/lib/galaxy/webapps/galaxy/controllers/data_admin.py:import simplejson
/usr/local/galaxy/lib/galaxy/webapps/galaxy/controllers/data_admin.py:        jsonjobs = simplejson.dumps( jobs )
/usr/local/galaxy/lib/galaxy/webapps/galaxy/controllers/data_admin.py:        return trans.fill_template( '/admin/data_admin/ajax_status.mako', json=simplejson.dumps( jobs ) )
/usr/local/galaxy/lib/galaxy/webapps/demo_sequencer/framework/__init__.py:pkg_resources.require( "simplejson" )
/usr/local/galaxy/lib/galaxy/webapps/demo_sequencer/framework/__init__.py:import simplejson
/usr/local/galaxy/lib/galaxy/tools/genome_index/__init__.py:pkg_resources.require("simplejson")
/usr/local/galaxy/lib/galaxy/tools/genome_index/__init__.py:import simplejson
/usr/local/galaxy/lib/galaxy/tools/genome_index/__init__.py:                logloc = simplejson.load( fp )
/usr/local/galaxy/lib/galaxy/tools/genome_index/index_genome.py:pkg_resources.require("simplejson")
/usr/local/galaxy/lib/galaxy/tools/genome_index/index_genome.py:import simplejson
/usr/local/galaxy/lib/galaxy/tools/genome_index/index_genome.py:        simplejson.dump( self.locations, self.outfile )
8

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
9

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

Complete output from command python setup.py 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/setup.py", line 112, in <module>
        """
      File "/usr/lib/python2.7/distutils/core.py", line 151, in setup
        dist.run_commands()
      File "/usr/lib/python2.7/distutils/dist.py", line 953, in run_commands
        self.run_command(cmd)
      File "/usr/lib/python2.7/distutils/dist.py", line 972, in run_command
        cmd_obj.run()
      File "/usr/local/galaxy/.venv/local/lib/python2.7/site-packages/setuptools/command/egg_info.py", line 160, in run
        writer = ep.load(installer=installer)
      File "/usr/local/galaxy/.venv/local/lib/python2.7/site-packages/pkg_resources.py", line 2188, in load
        self.require(env, installer)
      File "/usr/local/galaxy/.venv/local/lib/python2.7/site-packages/pkg_resources.py", line 2202, in require
        items = working_set.resolve(reqs, env, installer)
      File "/usr/local/galaxy/.venv/local/lib/python2.7/site-packages/pkg_resources.py", 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 setup.py egg_info" failed with error code 1 in /tmp/pip-install-BQINXC/beaker/
1 Like
10

Hi, Avoid the release still in development. The current stable Galaxy release is now 19.01. January 2019 Galaxy Release (v 19.01) — Galaxy Project 23.1.1.dev0 documentation

11

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
12

ping @nsoranzo @nate

13

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