Question: Two Administration Questions
gravatar for Assaf Gordon
10.5 years ago by
Assaf Gordon320
United States
Assaf Gordon320 wrote:
Hello, I have two administration-related questions: 1. I have a tool which uses dynamic options from an external file. A cron script updates this file, but the updated data doesn't appear in the tool's list-box until galaxy is restarted. Is there a way to re-load an option file without restarting galaxy? 2. In order to do some routine galaxy maintenance, I need to stop the daemon - Is there way to make sure no jobs are currently running before stopping the daemon? Thanks, Gordon.
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ADD COMMENTlink modified 10.5 years ago by Greg Von Kuster840 • written 10.5 years ago by Assaf Gordon320
gravatar for Greg Von Kuster
10.5 years ago by
Greg Von Kuster840 wrote:
Hello Assaf, The Galaxy admin page ( <your galaxy="" url="">/admin ) enables you to reload a tool while Galaxy is running. The admin password is configured in the main Galaxy config, and must be entered each time you reload a tool. The way to do this depends on the job runner(s) that are currently being used ( if any ). If the PBS job runner is being used, you can use the qstat command from the command line, something like this. If there are jobs running on the cluster, the Galaxy server can still be stopped and restarted and Galaxy will find the running jobs and re-add them to the Galaxy job queue. g2main@frisell:~$ qstat Job id Name User Time Use S Queue 102602.lonnie 174202 g2main 172:43:5 R batch 102748.lonnie 174335 g2main 168:02:4 R batch 103673.lonnie 175134 g2main 121:24:0 R batch 103675.lonnie 175135 g2main 121:22:2 R batch Another option is to perform a select from your database, something like the following. I will have a Galaxy report added to the code base shortly that will show this information as well. g2main@frisell:~$ psql galaxy_main Welcome to psql 8.1.11, the PostgreSQL interactive terminal. Type: \copyright for distribution terms \h for help with SQL commands \? for help with psql commands \g or terminate with semicolon to execute query \q to quit galaxy_main=> select id, state from job where state = 'new' or state = 'queued' or state = 'running'; id | state 174202 | running 174335 | running 175134 | running 175135 | running (4 rows) The local job runner may be a bit trickier. If you are using the local job runner for data retrieval from external sources, a "ps" is probably the best option. If you stop Galaxy while a job is running on the local job runner, that job will be stopped in an "error" state. g2main@frisell:~$ ps -ef | grep python g2main 12519 1 4 Jun06 ? 03:46:33 python -ES ./scripts/ serve universe_wsgi.ini --daemon
ADD COMMENTlink written 10.5 years ago by Greg Von Kuster840
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