Hi, I am running into an error that I bet has a simple solution. I would appreciate any help.  Thanks.

I am running Brad Chapman's LIMS extension locally on Ubuntu 12.  I also installed it as a service under /etc/init.d/chapman-galaxy using contrib/galaxy.debian-init .  It works when I run it directly (./run.sh --reload)

When I run a version of Galaxy without nglims as a service, there is no error.

When I run a version of Galaxy with nglims, not as a service (run.sh), there is no error.

However, when I run the same version of Galaxy with nglims as a service, there is an error.  I don't understand well enough what the difference is when I run it as a service to diagnose this problem.  The lines leading to the error from the log file is below.  Something to do with yaml not being loaded, but I know I installed python-yaml through aptitude.

galaxy.web.framework.base DEBUG 2013-06-14 09:46:26,873 Enabling 'requests' controller, class: Requests

galaxy.webapps.galaxy.controllers library_common galaxy.webapps.galaxy.controllers.library_common

galaxy.web.framework.base DEBUG 2013-06-14 09:46:26,874 Enabling 'library_common' controller, class: LibraryCommon

galaxy.webapps.galaxy.controllers nglims galaxy.webapps.galaxy.controllers.nglims

Traceback (most recent call last):

  File "./scripts/paster.py", line 34, in <module>

    command.run()

  File "/home/galaxy/bin/chapman-dist/eggs/PasteScript-1.7.3-py2.7.egg/paste/script/command.py", line 84, in run

    invoke(command, command_name, options, args[1:])

  File "/home/galaxy/bin/chapman-dist/eggs/PasteScript-1.7.3-py2.7.egg/paste/script/command.py", line 123, in invoke

    exit_code = runner.run(args)

  File "/home/galaxy/bin/chapman-dist/eggs/PasteScript-1.7.3-py2.7.egg/paste/script/command.py", line 218, in run

    result = self.command()

  File "/home/galaxy/bin/chapman-dist/eggs/PasteScript-1.7.3-py2.7.egg/paste/script/serve.py", line 276, in command

    relative_to=base, global_conf=vars)

  File "/home/galaxy/bin/chapman-dist/eggs/PasteScript-1.7.3-py2.7.egg/paste/script/serve.py", line 313, in loadapp

    **kw)

  File "/home/galaxy/bin/chapman-dist/eggs/PasteDeploy-1.3.3-py2.7.egg/paste/deploy/loadwsgi.py", line 204, in loadapp

    return loadobj(APP, uri, name=name, **kw)

  File "/home/galaxy/bin/chapman-dist/eggs/PasteDeploy-1.3.3-py2.7.egg/paste/deploy/loadwsgi.py", line 225, in loadobj

    return context.create()

  File "/home/galaxy/bin/chapman-dist/eggs/PasteDeploy-1.3.3-py2.7.egg/paste/deploy/loadwsgi.py", line 625, in create

    return self.object_type.invoke(self)

  File "/home/galaxy/bin/chapman-dist/eggs/PasteDeploy-1.3.3-py2.7.egg/paste/deploy/loadwsgi.py", line 188, in invoke

    filtered = context.next_context.create()

  File "/home/galaxy/bin/chapman-dist/eggs/PasteDeploy-1.3.3-py2.7.egg/paste/deploy/loadwsgi.py", line 625, in create

    return self.object_type.invoke(self)

  File "/home/galaxy/bin/chapman-dist/eggs/PasteDeploy-1.3.3-py2.7.egg/paste/deploy/loadwsgi.py", line 110, in invoke

    return fix_call(context.object, context.global_conf, **context.local_conf)

  File "/home/galaxy/bin/chapman-dist/eggs/PasteDeploy-1.3.3-py2.7.egg/paste/deploy/util/fixtypeerror.py", line 57, in fix_call

    val = callable(*args, **kw)

  File "/home/galaxy/bin/chapman-dist/lib/galaxy/webapps/galaxy/buildapp.py", line 44, in app_factory

    webapp.add_ui_controllers( 'galaxy.webapps.galaxy.controllers', app )

  File "/home/galaxy/bin/chapman-dist/lib/galaxy/web/framework/__init__.py", line 274, in add_ui_controllers

    module = import_module( module_name )

  File "/home/galaxy/bin/chapman-dist/lib/galaxy/util/backports/importlib/__init__.py", line 37, in import_module

    __import__(name)

  File "/home/galaxy/bin/chapman-dist/lib/galaxy/webapps/galaxy/controllers/nglims.py", line 24, in <module>

    import yaml

ImportError: No module named yaml