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
and the tool is not recognized. For the run.sh to work again i have to reboot my pc. In a virtual machine ubuntu image it's even worse. The 'run.sh' command keeps sending this error even when i reboot the image or even when i reboot the pc itself. Is there a way around this problem?
Thank you, Makis
2011/12/14 Makis Ladoukakis makis4ever@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
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 +0000 Subject: Re: [galaxy-dev] New tool not recognised unless i reboot From: p.j.a.cock@googlemail.com To: makis4ever@hotmail.com CC: galaxy-dev@lists.bx.psu.edu
2011/12/14 Makis Ladoukakis makis4ever@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
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 +0000 Subject: Re: [galaxy-dev] New tool not recognised unless i reboot From: p.j.a.cock@googlemail.com To: makis4ever@hotmail.com CC: galaxy-dev@lists.bx.psu.edu
2011/12/14 Makis Ladoukakis makis4ever@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
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Daniel Blankenberg -
Makis Ladoukakis -
Peter Cock