1. When you sudo you have to make sure the root user has JAVA_HOME set (via .bashrc, .profile, etc.), otherwise BioMart will not run. Just check "sudo echo $JAVA_HOME" an make sure it has a proper path.
2. Could be that user processes are killed on logout? Check your .logout file and maybe /etc/bash.logout (if you are using bash). This is very system specific so it's hard to tell what's going on. -jack From: Isaac cano <[email protected]<mailto:[email protected]>> Date: Wed, 6 Jul 2011 11:57:08 -0400 To: Jack Hsu <[email protected]<mailto:[email protected]>> Cc: BioMart Users <[email protected]<mailto:[email protected]>> Subject: Re: [BioMart Users] biomart-server.sh start problem Hi Jack, 1. Now running the script from de biomart home (./dist/scripts/biomart-server.sh) the command works, but only as root or another user, no using sudo. In this case I get the error that JAVA_HOME is not set. I've tried several things to keep JAVA_HOME set when using sudo but no way. Could you advise me on this? 2. I still have the problem that server shuts down when logging out as root or another user. Another biomart user told me that he is using sudo to start the server and it keeps alive after logging but I cannot confirm it because the above problem. Thanks for your help! Isaac 2011/7/5 Jack Hsu <[email protected]<mailto:[email protected]>> Hi Isaac, 1. How are you running the script? Can you try running it from within the "dist" directory? ./scripts/biomart-server.sh restart I would also check the logs under "dist/logs" for any errors that may have occurred. Look for a file starting with stdouterr. 2. The biomart-server.sh script should be running the server as a daemon process, so screen is not necessary. Logging out from your SSH session should be affect the process. Can you check that the process has indeed been killed? "ps aux | grep biomart" Also, the session.timeout is for a user session in the browser (cookie-based). It will not affect server operations. :) -jack From: Isaac cano <[email protected]<mailto:[email protected]>> Date: Tue, 5 Jul 2011 03:50:16 -0400 To: BioMart Users <[email protected]<mailto:[email protected]>> Subject: [BioMart Users] biomart-server.sh start problem Dear Biomart Users, I'm trying to set up a prototype using Biomart over a mysql database and I'm facing some problems when starting the server and trying to keep the server up for a long time (As an operating system I'm using Suse 10 and the Biomart version is 0.8 release candidate 6): 1. The first thing I would like to ask you is why I can run the server through martconfigurator (loading the registry file and then starting the server) but if I try to do the same using the "biomart-server.sh start/restart" command the server doesn't start I get the following message in the web browser: HTTP ERROR: 404 Problem accessing /. Reason: NOT_FOUND ________________________________ Powered by Jetty:// The output of the "biomart-server.sh start" command is the following: Shutting down BioMart: 24945 Starting BioMart: nohup: appending output to `nohup.out' BioMart running pid=25125 I've checked that the application settings point to the correct registry file (test): ################################################## # BIOMART APPLICATION SETTINGS ################################################## biomart.debug = false biomart.registry.file=/root/test biomart.registry.key.file=/root/.test biomart.sidebar = true 2. The other issue is how to keep the server up. I'm connecting to the server via ssh and I'm using the screen command to start the server (via martconfigurator) and then I detach the screen to keep the process running. Then I realised that when closing the ssh connection (putty) the server is usually down. Could you advice me about this issue? Just one additional thing, I realised that the is a session.timeout setting that I commented to prevent the server to go down after the specified amount of seconds. I really appreciate your help, Isaac Cano -- Isaac Cano Bioinformatics Linkcare Health Services SL C/Villarroel 170 08036 - Barcelona Tel.: (+34)932 275 400, ext. 4182\4523 Mobile: (+34) 666 186 748 Fax: (+34) 932 275 455 [email protected]<mailto:[email protected]>
_______________________________________________ Users mailing list [email protected] https://lists.biomart.org/mailman/listinfo/users
