Can't seem to stop or restart the Galaxy in server
Hello Everyone. Ctrl+C or Ctrl+D doesn't stop the Galaxy server. In local machine, I need to close the terminal and restart the terminal again. However, in server I integrated several tools, now I need to restart the server to test it. I used ./run.sh --reload doesn't restart the server and I can't stop the server. How can I stop or restart Galaxy in the real working server? Thanks
With a certain version of Python there's been an issue stopping Galaxy using ctrl+C. You can use 'sh run.sh --daemon' to have the process run in the background and then 'sh run.sh --stop-damemon' to stop it. Hope this helps, Enis On Thu, Oct 18, 2012 at 4:12 PM, Sachit Adhikari < sachit.technerves@gmail.com> wrote:
Hello Everyone. Ctrl+C or Ctrl+D doesn't stop the Galaxy server. In local machine, I need to close the terminal and restart the terminal again. However, in server I integrated several tools, now I need to restart the server to test it. I used ./run.sh --reload doesn't restart the server and I can't stop the server. How can I stop or restart Galaxy in the real working server? Thanks ___________________________________________________________ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list:
http://lists.bx.psu.edu/listinfo/galaxy-dev
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Thanks. Helped me! On Thu, Oct 18, 2012 at 11:02 AM, Enis Afgan <eafgan@emory.edu> wrote:
With a certain version of Python there's been an issue stopping Galaxy using ctrl+C. You can use 'sh run.sh --daemon' to have the process run in the background and then 'sh run.sh --stop-damemon' to stop it.
Hope this helps, Enis
On Thu, Oct 18, 2012 at 4:12 PM, Sachit Adhikari < sachit.technerves@gmail.com> wrote:
Hello Everyone. Ctrl+C or Ctrl+D doesn't stop the Galaxy server. In local machine, I need to close the terminal and restart the terminal again. However, in server I integrated several tools, now I need to restart the server to test it. I used ./run.sh --reload doesn't restart the server and I can't stop the server. How can I stop or restart Galaxy in the real working server? Thanks ___________________________________________________________ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list:
http://lists.bx.psu.edu/listinfo/galaxy-dev
To manage your subscriptions to this and other Galaxy lists, please use the interface at:
Yes, daemon/stop-daemon is the best way. However, to stop a process that was not started with --daemon, this is what I do: ps aux | grep galaxy Identify the process numbers for 3 Galaxy processes, which will change every time Galaxy is restarted. For example this line: galaxy 11638 0.0 0.0 63856 988 ? S Nov10 0:00 /bin/sh ./run.sh --reload indicates the process has a number of 11638. The 3 processes look like: /bin/sh ./run.sh --reload python ./scripts/paster.py serve universe_wsgi.ini --reload /home/galaxy/bin/python ./scripts/paster.py serve universe_wsgi.ini --reload Next, kill the three processes with this command: kill -9 <ID1> <ID2> <ID3> On Oct 17, 2012, at 10:17 PM, Enis Afgan wrote:
With a certain version of Python there's been an issue stopping Galaxy using ctrl+C. You can use 'sh run.sh --daemon' to have the process run in the background and then 'sh run.sh --stop-damemon' to stop it.
Hope this helps, Enis
On Thu, Oct 18, 2012 at 4:12 PM, Sachit Adhikari <sachit.technerves@gmail.com> wrote: Hello Everyone. Ctrl+C or Ctrl+D doesn't stop the Galaxy server. In local machine, I need to close the terminal and restart the terminal again. However, in server I integrated several tools, now I need to restart the server to test it. I used ./run.sh --reload doesn't restart the server and I can't stop the server. How can I stop or restart Galaxy in the real working server? Thanks ___________________________________________________________ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list:
http://lists.bx.psu.edu/listinfo/galaxy-dev
To manage your subscriptions to this and other Galaxy lists, please use the interface at:
___________________________________________________________ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list:
http://lists.bx.psu.edu/listinfo/galaxy-dev
To manage your subscriptions to this and other Galaxy lists, please use the interface at:
On Oct 18, 2012, at 1:43 AM, Todd Oakley wrote:
Yes, daemon/stop-daemon is the best way. However, to stop a process that was not started with --daemon, this is what I do:
ps aux | grep galaxy
Identify the process numbers for 3 Galaxy processes, which will change every time Galaxy is restarted. For example this line: galaxy 11638 0.0 0.0 63856 988 ? S Nov10 0:00 /bin/sh ./run.sh --reload
indicates the process has a number of 11638. The 3 processes look like: • /bin/sh ./run.sh --reload • python ./scripts/paster.py serve universe_wsgi.ini --reload • /home/galaxy/bin/python ./scripts/paster.py serve universe_wsgi.ini --reload Next, kill the three processes with this command: kill -9 <ID1> <ID2> <ID3>
Hi Todd, Are you unable to Ctrl+C when using --reload? Using --reload is actually my workaround for this problem. --nate
On Oct 17, 2012, at 10:17 PM, Enis Afgan wrote:
With a certain version of Python there's been an issue stopping Galaxy using ctrl+C. You can use 'sh run.sh --daemon' to have the process run in the background and then 'sh run.sh --stop-damemon' to stop it.
Hope this helps, Enis
On Thu, Oct 18, 2012 at 4:12 PM, Sachit Adhikari <sachit.technerves@gmail.com> wrote: Hello Everyone. Ctrl+C or Ctrl+D doesn't stop the Galaxy server. In local machine, I need to close the terminal and restart the terminal again. However, in server I integrated several tools, now I need to restart the server to test it. I used ./run.sh --reload doesn't restart the server and I can't stop the server. How can I stop or restart Galaxy in the real working server? Thanks ___________________________________________________________ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list:
http://lists.bx.psu.edu/listinfo/galaxy-dev
To manage your subscriptions to this and other Galaxy lists, please use the interface at:
___________________________________________________________ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list:
http://lists.bx.psu.edu/listinfo/galaxy-dev
To manage your subscriptions to this and other Galaxy lists, please use the interface at:
___________________________________________________________ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list:
http://lists.bx.psu.edu/listinfo/galaxy-dev
To manage your subscriptions to this and other Galaxy lists, please use the interface at:
I have had it happen occasionally, but didn't pay attention to the details. Perhaps I forget to put --reload sometimes. Also, it seems that sometimes the Galaxy processes do not all stop with --stop-daemon. I wrote the text below as a recipe for people in my lab to restart in those situations, and I copied it here... On 10/19/2012 8:24 AM, Nate Coraor wrote:
On Oct 18, 2012, at 1:43 AM, Todd Oakley wrote:
Yes, daemon/stop-daemon is the best way. However, to stop a process that was not started with --daemon, this is what I do:
ps aux | grep galaxy
Identify the process numbers for 3 Galaxy processes, which will change every time Galaxy is restarted. For example this line: galaxy 11638 0.0 0.0 63856 988 ? S Nov10 0:00 /bin/sh ./run.sh --reload
indicates the process has a number of 11638. The 3 processes look like: • /bin/sh ./run.sh --reload • python ./scripts/paster.py serve universe_wsgi.ini --reload • /home/galaxy/bin/python ./scripts/paster.py serve universe_wsgi.ini --reload Next, kill the three processes with this command: kill -9 <ID1> <ID2> <ID3> Hi Todd,
Are you unable to Ctrl+C when using --reload? Using --reload is actually my workaround for this problem.
--nate
On Oct 17, 2012, at 10:17 PM, Enis Afgan wrote:
With a certain version of Python there's been an issue stopping Galaxy using ctrl+C. You can use 'sh run.sh --daemon' to have the process run in the background and then 'sh run.sh --stop-damemon' to stop it.
Hope this helps, Enis
On Thu, Oct 18, 2012 at 4:12 PM, Sachit Adhikari <sachit.technerves@gmail.com> wrote: Hello Everyone. Ctrl+C or Ctrl+D doesn't stop the Galaxy server. In local machine, I need to close the terminal and restart the terminal again. However, in server I integrated several tools, now I need to restart the server to test it. I used ./run.sh --reload doesn't restart the server and I can't stop the server. How can I stop or restart Galaxy in the real working server? Thanks ___________________________________________________________ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list:
http://lists.bx.psu.edu/listinfo/galaxy-dev
To manage your subscriptions to this and other Galaxy lists, please use the interface at:
___________________________________________________________ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list:
http://lists.bx.psu.edu/listinfo/galaxy-dev
To manage your subscriptions to this and other Galaxy lists, please use the interface at:
The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list:
http://lists.bx.psu.edu/listinfo/galaxy-dev
To manage your subscriptions to this and other Galaxy lists, please use the interface at:
-- *************************************** Todd Oakley, Professor Ecology Evolution and Marine Biology University of California, Santa Barbara Santa Barbara, CA 93106 USA *************************************** Lab Website <http://labs.eemb.ucsb.edu/oakley/todd/> Twitter: @UCSB_OakleyLab *Recent Papers: * * Pancrustacean Phylotranscriptomics MBE Paper <http://mbe.oxfordjournals.org/content/early/2012/09/12/molbev.mss216.abstract> * Convergent Evolution in Cephalopoda BMC Ev Biol <http://www.biomedcentral.com/1471-2148/12/129/abstract> * Cnidocyte discharge regulated by opsin and light BMC Biology Paper <http://tinyurl.com/7dajl2q> Scientific American Write-up <http://blogs.scientificamerican.com/science-sushi/2012/03/05/hydra-watch-what-they-eat/> * Sponge Larvae Could be Guided by Cryptochrome J Exp Biol. Paper <http://jeb.biologists.org/content/215/8/ii> | Nature News <http://www.nature.com/nature/journal/v484/n7393/full/484145d.html>
participants (4)
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Enis Afgan -
Nate Coraor -
Sachit Adhikari -
Todd Oakley