Recover Galaxy after Virtual Machine reboot

How to correctly restart Galaxy after a reboot of the Virtual Machine ?

After the boot procedure of your VM at least these services should already be up and running:

  1. PostgreSQL
  2. Proftpd
  3. NGINX

Trying to connect to your Galaxy instance IP with a web browser you should see:

Galaxy page

Step 1: Unlock encrypted storage

If your instance is not mounted on encrypted storage please skip this and go to Step 2: One-command procedure

To unlock the volume connect with SSH and type the command sudo /usr/local/bin/luksctl open followed by your passphrase.

$ sudo /usr/local/bin/luksctl open
Enter passphrase for /dev/disk/by-uuid/4ba96890-f914-46aa-b7a6-7e71f0846f43:

Name:              jzwoejuw
State:             ACTIVE
Read Ahead:        8192
Tables present:    LIVE
Open count:        1
Event number:      0
Major, minor:      252, 0
Number of targets: 1
UUID: CRYPT-LUKS1-4ba96890f91446aab7a67e71f0846f43-jzwoejuw

Encrypted volume: [ OK ]

Step 2: One-command procedure

To start Galaxy you can just copy and paste this:

$ sudo su -c "wget -O - https://raw.githubusercontent.com/Laniakea-elixir-it/Scripts/master/galaxy/recover.sh | bash" root

Probing /cvmfs/elixir-italy.galaxy.refdata... OK
Contacting Galaxy (wait for 10 seconds)...
Galaxy server on-line: [ OK ]

Warning

This may require few minutes, but should safely restart your Galaxy.

Galaxy page

Advanced Step-by-step procedure

Warning

Please follow this instructions only if you know what you are doing!

Mount reference data

After encrypion storage unlock (see section Step 1: Unlock encrypted storage), if you have it, you need now to mount your reference datasets:

$ sudo systemctl restart autofs

$ sudo cvmfs_config killall

Terminating cvmfs_config processes... OK
Terminating cvmfs2 processes... OK
Unmounting stale mount points... OK
Cleaning up run-time variable data... OK
Reloading autofs... OK

$ sudo cvmfs_config probe

Probing /cvmfs/elixir-italy.galaxy.refdata... OK

Start Galaxy

Finally, to correctly start all Galaxy services run: sudo /usr/local/bin/galaxy-startup

$ sudo /usr/local/bin/galaxy-startup

Loading Galaxy environment
Exporting environment variables
Check if galaxy is up and running, to avoid unuseful restart
status: 502
Galaxy unreachable
Check is supervisord is running
Starting the Galaxy production environment
/usr/lib/python2.7/site-packages/supervisor/options.py:383: PkgResourcesDeprecationWarning: Parameters to load are deprecated.  Call .resolve and .require separately.
return pkg_resources.EntryPoint.parse("x="+spec).load(False)

Galaxy start: [ OK ]