nglims/services/python

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nglims/services/python

Lee Katz
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


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Re: nglims/services/python

Ross-2
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 <[hidden email]> 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




___________________________________________________________
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in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
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Re: nglims/services/python

Lee Katz
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 <[hidden email]> 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 <[hidden email]> 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 <[hidden email]> 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.

___________________________________________________________
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:
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Re: nglims/services/python

Lee Katz
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 <[hidden email]> 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 <[hidden email]> 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 <[hidden email]> 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 <[hidden email]> 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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