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