Difference between revisions of "Restarting Galaxy"
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| + | == Most reliable way to restart galaxy2 as of July 4, 2017: == | ||
| + | |||
| + | # [[Connect to knot using the galaxy user login]] | ||
| + | # Then change to the galaxy-dist directory: | ||
| + | #: cd galaxy2/galaxy-dist | ||
| + | #: ./restart.sh | ||
| + | |||
| + | == Other ways to do restart Galaxy == | ||
| + | There are two other methods to restart the Galaxy server if the restart.sh script does not work. | ||
| + | |||
| + | The first (old) method is to use nohup. | ||
| + | The preferred method is to run Galaxy as a daemon process. | ||
| + | |||
| + | You may have to kill Galaxy manually if someone used the nohup method to start Galaxy. | ||
| + | |||
| + | === Killing Galaxy Using the Daemon Method === | ||
| + | |||
| + | # [[Connect to knot using the galaxy user login]] | ||
| + | # Then change to the galaxy-dist directory: | ||
| + | #: cd galaxy2/galaxy-dist | ||
| + | # Then stop the Galaxy daemon: | ||
| + | #: ./run.sh --stop-daemon | ||
| + | |||
| + | === Starting Galaxy Up Again === | ||
| + | |||
# [[Connect to knot using the galaxy user login]] | # [[Connect to knot using the galaxy user login]] | ||
| − | # Find the galaxy processs that are running by typing: | + | # Then change to the galaxy-dist directory: |
| − | ps aux | grep galaxy | + | #: cd galaxy2/galaxy-dist |
| − | + | # Then start the Galaxy daemon: | |
| + | #: ./run.sh --reload --daemon | ||
| + | |||
| + | If this method does not work, use the manual method below. | ||
| + | |||
| + | |||
| + | === Killing Galaxy Manually (old) === | ||
| + | Only use this method if the daemon method does not work. | ||
| + | |||
| + | [[Connect to knot using the galaxy user login]] | ||
| + | Find the galaxy processs that are running by typing: | ||
| + | ps aux | grep galaxy | ||
| + | Identify the process numbers for 3 Galaxy processes, which will change every time Galaxy is restarted. | ||
For example this line: | For example this line: | ||
| − | galaxy 11638 0.0 0.0 63856 988 ? S Nov10 0:00 /bin/sh ./run.sh --reload | + | 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. | indicates the process has a number of 11638. | ||
The 3 processes look like: | 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> | + | kill -9 <ID1> <ID2> <ID3> |
| − | |||
Latest revision as of 21:25, 7 August 2017
Contents
Most reliable way to restart galaxy2 as of July 4, 2017:[edit]
- Connect to knot using the galaxy user login
- Then change to the galaxy-dist directory:
- cd galaxy2/galaxy-dist
- ./restart.sh
Other ways to do restart Galaxy[edit]
There are two other methods to restart the Galaxy server if the restart.sh script does not work.
The first (old) method is to use nohup. The preferred method is to run Galaxy as a daemon process.
You may have to kill Galaxy manually if someone used the nohup method to start Galaxy.
Killing Galaxy Using the Daemon Method[edit]
- Connect to knot using the galaxy user login
- Then change to the galaxy-dist directory:
- cd galaxy2/galaxy-dist
- Then stop the Galaxy daemon:
- ./run.sh --stop-daemon
Starting Galaxy Up Again[edit]
- Connect to knot using the galaxy user login
- Then change to the galaxy-dist directory:
- cd galaxy2/galaxy-dist
- Then start the Galaxy daemon:
- ./run.sh --reload --daemon
If this method does not work, use the manual method below.
Killing Galaxy Manually (old)[edit]
Only use this method if the daemon method does not work.
Connect to knot using the galaxy user login Find the galaxy processs that are running by typing:
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>
