[galaxy-dev] abolut ftp setup
Dear all, I'm a student at Fudan University in China. I was trying to enable ftp uploading in my local version of GALAXY. I tried the setting in http://wiki.g2.bx.psu.edu/Admin/Config/Upload%20via%20FTP, but I got the following problems: 1. The galaxyftp seems to be a pasql database, shall I build it myself? or does it already exists in galaxy directory? 2. the galaxy_user seems to be a table, shall I build it myself? and how shall I update it and integrate it with galaxy? Thanks for your attention, and looking forward to your reply! Best wishes Liao Ruiqi ___ 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/
[galaxy-dev] Job runner out of memory problem
It seems that even under very light i.e. just a couple of long-running jobs present load the job runner slowly, but steadily (1-3Mb per sec) grows its memory consumption until it's killed by linux OOM killer. My job runner config: http://pastebin.com/vMWDHAQm I'm currently restarting the runner out of crontab when it is killed by OOM, but it's not a sensible solution by any means. I wonder if anyone encountered this and how it was solved. Thanks, Alex ___ 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/
Re: [galaxy-dev] New tool not recognised unless i reboot
I couldn't find a way to stop the instance through the terminal. Ctrl+C doesn't work so i just close the terminal itself. Is there a command that stops the instance? Date: Wed, 14 Dec 2011 17:32:41 + Subject: Re: [galaxy-dev] New tool not recognised unless i reboot From: p.j.a.c...@googlemail.com To: makis4e...@hotmail.com CC: galaxy-dev@lists.bx.psu.edu 2011/12/14 Makis Ladoukakis makis4e...@hotmail.com: Dear galaxy users, I have downloaded a local instance of Galaxy on my linux distribution (ubuntu) and i am adding new tools i made myself. To add a new tool i follow all the steps (tool definition file and the modification of tool_conf.xml) and run 'sh run.sh' for Galaxy to include it in its interface. Nevertheless when i try to do the same later after i close Galaxy, when i run 'sh run.sh' again i get this error: socket.error: [Errno 98] Address already in use Did you stop the old Galaxy instance which is still running and using that network address? Peter ___ 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/
Re: [galaxy-dev] New tool not recognised unless i reboot
Hi Makis, Ordinarily in interactive mode, ctrl+c should work. However, when just using 'run.sh' certain python/OS combinations experience issues. You'll need to manually kill your instance, e.g. using 'kill pid'. Next time you start Galaxy you can use 'run.sh --reload' which should enable interactive usage with ctrl-c working. You can also stat Galaxy daemonized using 'sh run.sh --daemon'; stop with sh run.sh --stop-daemon'. Thanks for using Galaxy, Dan On Dec 14, 2011, at 3:36 PM, Makis Ladoukakis wrote: I couldn't find a way to stop the instance through the terminal. Ctrl+C doesn't work so i just close the terminal itself. Is there a command that stops the instance? Date: Wed, 14 Dec 2011 17:32:41 + Subject: Re: [galaxy-dev] New tool not recognised unless i reboot From: p.j.a.c...@googlemail.com To: makis4e...@hotmail.com CC: galaxy-dev@lists.bx.psu.edu 2011/12/14 Makis Ladoukakis makis4e...@hotmail.com: Dear galaxy users, I have downloaded a local instance of Galaxy on my linux distribution (ubuntu) and i am adding new tools i made myself. To add a new tool i follow all the steps (tool definition file and the modification of tool_conf.xml) and run 'sh run.sh' for Galaxy to include it in its interface. Nevertheless when i try to do the same later after i close Galaxy, when i run 'sh run.sh' again i get this error: socket.error: [Errno 98] Address already in use Did you stop the old Galaxy instance which is still running and using that network address? Peter ___ 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/ ___ 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/
[galaxy-dev] Executing a binary file from Galaxy job
Hi, I have a perl script which executes a Java JAR file located in tool-data/shared/jars/ and this Jar file at one point executes 2 other binary programs during its job process. These 2 programs are located in the same directory as the JAR file. I am getting errors in Galaxy saying No such file or directory when these 2 external programs are called. I am assuming this is the case because they are not located in current working directory of the current Galaxy job process. Is there a way to somehow redirect Galaxy into the correct directory where the binary files are located? Thanks. ___ 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/
