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 <lskatz@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.lazarus@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.lazarus@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 <lskatz@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.