Hi Loraine, It looks like you have a copy of Galaxy already running on that port. If you are just using the command 'sh run.sh' to run Galaxy, it is not being run as a daemon, so that '--stop-daemon' will not stop the already running server. You can use 'ctrl-c' to stop the server that you have started within a console. If you don't have access to the console view of this (e.g. you did a 'sh run.sh &'), you can do: $ ps x | grep "python ./scripts/paster.py serve universe_wsgi.ini" 13294 s001 S+ 14:25.14 python ./scripts/paster.py serve universe_wsgi.ini 20592 s003 S+ 0:00.00 grep python ./scripts/paster.py serve universe_wsgi.ini and then kill the process directly (e.g. 'kill 13294') To run Galaxy as a daemon start it like 'sh run.sh --daemon', then you can use 'sh run.sh --stop-daemon' to end it later. Thanks for using Galaxy, Dan On May 7, 2010, at 5:31 AM, Loraine Brillet wrote:
Hello,
I would like to add a new tool to my local Galaxy install but I fail. I have put the script and the xml description file in the tools/ directory and modified the tool_conf.xml file. I type sh run.sh and the end of the message on the screen is : socket.error: (98, 'Address already in use') galaxy.jobs INFO 2010-05-07 11:19:20,397 sending stop signal to worker thread galaxy.jobs INFO 2010-05-07 11:19:20,397 job queue stopped galaxy.jobs.runners.local INFO 2010-05-07 11:19:20,397 sending stop signal to worker threads galaxy.jobs.runners.local INFO 2010-05-07 11:19:20,398 local job runner stopped galaxy.jobs INFO 2010-05-07 11:19:20,398 sending stop signal to worker thread galaxy.jobs INFO 2010-05-07 11:19:20,398 job stopper stopped
and the new tool was not available on the refreshed page of the browser.
The script being already running , I thought that could be problem (Am I right ?) and tried "run.sh --stop-daemon", which returned me "No PID file exists in paster.pid".
What is the right thing to do ?
Thanks for your help,
Loraine
-- Loraine Brillet
Service Informatique et Genomique Plateforme ABiMS (Analyses and Bioinformatics for Marine Sciences) Station Biologique de Roscoff FR 2424 CNRS UPMC Place Georges Teissier 29682 Roscoff Cedex tel: ++33 (0)2 98 29 25 50 fax: ++33 (0)2 98 29 23 24 email: loraine.brillet@sb-roscoff.fr http://www.sb-roscoff.fr http://www.sb-roscoff.fr/abims/
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