Hi Nate, I am sorry I missed your reply... Thanks for your input, will try this soon. Cheers, Joachim Joachim Jacob Rijvisschestraat 120, 9052 Zwijnaarde Tel: +32 9 244.66.34 Bioinformatics Training and Services (BITS) http://www.bits.vib.be @bitsatvib On 02/13/2013 06:31 PM, Nate Coraor wrote:

On Feb 11, 2013, at 7:48 AM, Joachim Jacob |VIB| wrote:

...

Hello all,

After a *reboot* of our Galaxy server, the environment variables are set correctly.

However, after *restarting* the Galaxy process on a running server, by logging in as Galaxy and running the init script on CentOS as "service galaxyd restart", the environment variables seems to be messed up Hi Joachim,

It seems odd you'd be logging in as Galaxy to restart the process. Since the system is going to run the init script as root, you should do this as well when you restart it. Presumably whatever init script you are using is properly switching to the galaxy user to start the server process(es).

--nate

...

After this manual Galaxy restart, some tools are not found, apparently caused by a modification of the environment variable PATH. Can somebody provide me perhaps with insight on what is causing this, and how to avoid this?

My environment variables are set in /etc/profile.d/galaxy_environment_setup (which is a symbolic link to -> /home/galaxy/environment_setup )

Thanks, Joachim

-- Joachim Jacob

Rijvisschestraat 120, 9052 Zwijnaarde Tel: +32 9 244.66.34 Bioinformatics Training and Services (BITS) http://www.bits.vib.be @bitsatvib

___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at:

http://lists.bx.psu.edu/