Re: [galaxy-dev] nglims/services/python
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)
Re: [galaxy-dev] nglims/services/python
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
