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
> 
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