Can'T Seem To Stop Or Restart The Galaxy In Server

Question: Can'T Seem To Stop Or Restart The Galaxy In Server

6.1 years ago by

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

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modified 6.1 years ago by Enis Afgan • 680 • written 6.1 years ago by Sachit Adhikari • 320

6.1 years ago by

Enis Afgan • 680

Enis Afgan • 680 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 <

ADD COMMENT • link written 6.1 years ago by Enis Afgan • 680

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>

ADD REPLY • link written 6.1 years ago by Todd Oakley • 40

Hi Todd, Are you unable to Ctrl+C when using --reload? Using --reload is actually my workaround for this problem. --nate

ADD REPLY • link written 6.1 years ago by Nate Coraor ♦ 3.2k

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... -- *************************************** 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.mss="" 216.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="">

ADD REPLY • link written 6.1 years ago by Todd Oakley • 40

Thanks. Helped me!

ADD REPLY • link written 6.1 years ago by Sachit Adhikari • 320

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