I figured it out after some more digging. The /etc/init.d script had a
Python flag -S which narrows down the paths where Python will search for
modules. The path with pyaml was excluded and could not be found. So, I
removed the -S flag.
And then, I almost forgot to run the command to make it start up with the
reboot and so I will put it here for anyone who might find this post helpful
update-rc.d chapman-galaxy defaults
On Mon, Jun 17, 2013 at 9:24 AM, Lee Katz <lsk...@gmail.com> wrote:
> Thanks Ross! Unfortunately I still have the same error. Although I can
> directly run galaxy via the command run.sh, the system service fails with
> the error I showed before. In other words this works as the galaxy user:
> ./run.sh --restart
>
> This does not work when I run it as root (or when root runs it as the
> machine starts up):
> service chapman-galaxy start
>
> This is the init file which I slightly modified from the contrib directory
> (which now resides under /etc/init.d/). There must be some fundamental
> reason why running it as root does not work that I don't understand. I
> actually don't think it's this init script that is the problem because a
> vanilla install of Galaxy works fine using "system galaxy start" and when
> it is under init.d.
>
> #!/bin/bash
>
> # Author: James Casbon, 2009
> # Modified by Lee Katz 2013 for this specific system
>
> ### BEGIN INIT INFO
> # Provides: chapman-galaxy
> # Required-Start: $network $local_fs $mysql
> # Required-Stop:
> # Default-Start: 2 3 4 5
> # Default-Stop: 0 1 6
> # Short-Description: Chapman-Galaxy
> ### END INIT INFO
>
> . /lib/lsb/init-functions
>
> USER="galaxy"
> GROUP="galaxy"
> DIR="/home/galaxy/bin/chapman-dist"
> PYTHON="/usr/bin/python"
> OPTS="-ES ./scripts/paster.py serve --log-file $DIR/galaxy.log
> universe_wsgi.ini"
> PIDFILE="/var/run/galaxy-chapman.pid"
>
> case "${1:-''}" in
> 'start')
> log_daemon_msg "Starting Chapman-Galaxy"
> if start-stop-daemon --chuid $USER --group $GROUP --start
> --make-pidfile \
> --pidfile $PIDFILE --background --chdir $DIR --exec $PYTHON --
> $OPTS; then
> log_end_msg 0
> else
> log_end_msg 1
> fi
> ;;
> 'stop')
> log_daemon_msg "Stopping Chapman-Galaxy"
> if start-stop-daemon --stop --pidfile $PIDFILE; then
> log_end_msg 0
> else
> log_end_msg 1
> fi
> ;;
> 'restart')
> # restart commands here
> $0 stop
> $0 start
>
> ;;
> 'status')
> if [ -f "$PIDFILE" ]; then
> pid=`cat $PIDFILE`;
> log_daemon_msg "Chapman-galaxy pid is $pid"
> else
> log_daemon_msg "Chapman-galaxy does not have a pid"
> fi
> ;;
> *) # no parameter specified
> echo "Usage: $SELF start|stop|restart|reload|force-reload|status"
> exit 1
> ;;
> esac
>
>
>
>
>
> On Sat, Jun 15, 2013 at 12:38 AM, Ross <ross.laza...@gmail.com> wrote:
>
>> My mistake - try
>> (sudo) pip install pyaml
>> That's what the pip yaml repo is called...
>>
>>
>>
>> On Sat, Jun 15, 2013 at 11:38 AM, Ross <ross.laza...@gmail.com> wrote:
>>
>>> 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
>>>>
>>>>
>>>>
>>>>
>
>
> --
> Lee Katz, Ph.D.
>
--
Lee Katz, Ph.D.
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