Hi, Lee - the last line of that error dump might be worth thinking about. It seems clear enough. Your python interpreter seems unable to import a module called yaml
Perhaps you need to (eg) do pip install yaml in the virtualenv (or sudo ... for the system one if not using a virtualenv) you're running your Galaxies with? I hope this helps. On Fri, Jun 14, 2013 at 11:52 PM, Lee Katz <lsk...@gmail.com> wrote: > 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 > > > >
___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
