NBIC Galaxy Server: How to update NBIC Galaxy

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Galaxy start procedure at new HPC cloud

  1. go to https://ui.hpccloud.surfsara.nl/
  2. use template NBICGalaxy to instantiate a new VM with name "galaxy". Both disk images using for Galaxy are in persistent state, so all changes should be automatically saved.
  3. due to a problem with migration, you need to access the VM via VNC and restart eth0 and eth1 to get correct IP address
  4. Now you can start Galaxy system using the following commands.
ssh galaxy.nbic.nl

Check whether /var/run/postgresql exists and has the right owners. Otherwise create it:

sudo mkdir /var/run/postgresql/
sudo chown postgres:postgres /var/run/postgresql/

And start database, webserver and galaxy:≈

sudo su postgres
/usr/lib/postgresql/9.1/bin/pg_ctl start -o "-p 5840" -D /mnt/galaxyData/pgsql/data
sudo /opt/galaxy/pkg/nginx/sbin/nginx
sudo /bin/su - galaxy -c "export SGE_ROOT=/opt/sge; sh /mnt/galaxyTools/galaxy-central/run.sh --daemon"

Saving the image

The server runs on a persistent image. That means that when it is properly stopped and deployed, a restart will have all changes saved. However, if the server is stopped because of a hardware or power failure of the cloud node, it will NOT be saved. It is therefore a good idea to save a copy every once in a while after big updates or configuration changes.

  1. Log in on sara cloud
  2. Identify the running server.
  3. Using the "Pause" button select ""power off" and wait for POWEROFF state.
  4. Click on the name of the server, and the "Storage" tab
  5. In the line for the "vda" drive, click on the "Save as" icon/label
  6. Type "GalaxyMaster_yyyymmdd" as the name of the backup
  7. Wait for the save to complete (up to 15 minutes?)
  8. Restart the server using the "Play" button, and the services (see above)

See also: Obsolete instructions for Galaxy server on old HPC cloud