NBIC Galaxy Server: How to update NBIC Galaxy
Galaxy start procedure at new HPC cloud
- go to https://ui.hpccloud.surfsara.nl/
- 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.
- due to a problem with migration, you need to access the VM via VNC and restart eth0 and eth1 to get correct IP address
- Now you can start Galaxy system using the following commands.
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 exit 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.
- Log in on sara cloud
- Identify the running server.
- Using the "Pause" button select ""power off" and wait for POWEROFF state.
- Click on the name of the server, and the "Storage" tab
- In the line for the "vda" drive, click on the "Save as" icon/label
- Type "GalaxyMaster_yyyymmdd" as the name of the backup
- Wait for the save to complete (up to 15 minutes?)
- Restart the server using the "Play" button, and the services (see above)