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.
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