This is a test version of Biostars. For the public version, visit https://www.biostars.org.
Setup Galaxy Server As A Non-Root System Service

On the Galaxy server website for setting up a local server, they recommend setting up Galaxy to run as a NON-ROOT system service (excerpt below). Does anyone know how to do this? I am on CENTOS with the galaxy files set up in the home directory of non-root user "galaxy." I have been logging in remotely to start the script over ssh but I can see this is not ideal.

Suggestions appreciated. zach cp

Galaxy should be a managed system service (like Apache, mail servers, database servers, etc.) run by the galaxy user. Init scripts, OS X launchd definitions and Solaris SMF manifests are provided in the contrib/ directory of the distribution. You can also use the --daemon and --stop-daemon arguments to run.sh to start and stop by hand, but still run detached. When running as a daemon the server's output log will be written to paster.log instead of the terminal, unless instructed otherwise with the --log-file argument.

galaxy
• 8,010 views • link
updated by Nate • Nate • written by Zach Powers Zach Powers

2 answers

The best way to manage this is with an init script in /etc/init.d/galaxy. Here is an example template we use for Galaxy on CentOS:

The init script syntax and usage is not Galaxy specific, so any general tutorials for CentOS init scripts will be helpful:

http://articles.slicehost.com/2009/2/2/centos-adding-an-nginx-init-script

• 1 views • link
updated by Ram Ram • written by Brad Chapman Brad Chapman

Oh, I'll just steal this one, then... ;)

• 0 views • link
written by Nate • Nate

awesome! I like playing with code as much as the next man but it does seem that you can muck up your system pretty good with init scripts. thanks brad.

• 0 views • link
written by Zach Powers Zach Powers

Committed in b2bc0629e781.

• 0 views • link
written by Nate • Nate

Committed in b2bc0629e781. Thanks!

• 0 views • link
written by Nate • Nate

Nate, brilliant stuff. Thanks for putting this in so quickly. Zach, glad to help.

• 0 views • link
written by Brad Chapman Brad Chapman

just change /path/to/galaxy and chmod +x and you are good to go. worked like a charm. thanks guys.

• 0 views • link
written by Zach Powers Zach Powers

Hi Zach,

Hmm, the rc script in the contrib/ directory is for Debian and uses start-stop-daemon which is not available under Fedora derivatives. I'll drop a Fedora-friendly script in there momentarily.

--nate

• 1 views • link
written by Nate • Nate

thanks nate. You can use Brad's script.

• 0 views • link
written by Zach Powers Zach Powers

Log in to answer this question.

More posts like this