Restarting Galaxy

Most reliable way to restart galaxy2 as of July 4, 2017:

1. Connect to knot using the galaxy user login
2. 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

1. Connect to knot using the galaxy user login
2. Then change to the galaxy-dist directory:

   cd galaxy2/galaxy-dist

3. Then stop the Galaxy daemon:

   ./run.sh --stop-daemon

Starting Galaxy Up Again

1. Connect to knot using the galaxy user login
2. Then change to the galaxy-dist directory:

   cd galaxy2/galaxy-dist

3. 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:

 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:

1. /bin/sh ./run.sh --reload
2. python ./scripts/paster.py serve universe_wsgi.ini --reload
3. /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>