On Fri, Sep 3, 2010 at 4:20 PM, Nate Coraor <nate(a)bx.psu.edu> wrote:
I haven't ever tried without a real home directory or shell, but I don't
know of any reason you wouldn't be able to run like this if you're not
using a cluster.
I take it then that the "normal" way to install Galaxy is to create a
galaxy user, and put the files under /home/galaxy - if that is what
most installations do, I can follow suit.
I'm unclear how it is relevant, but we do have a cluster available,
although I'm not sure at this point if we would try and call it from
Galaxy... there are internal networking constraints which may
prevent that.
Please let us know if you encounter any more issues.
I've tried to setup an /etc/init.d/galaxy script for CentOS (having
looked at the examples in the galaxy-dist/contrib folder), and
have something which seems to be working using:
...
. /etc/init.d/functions
start () {
daemon --user galaxy "/opt/galaxy-dist/run.sh --daemon"
}
stop() {
daemon --user galaxy "/opt/galaxy-dist/run.sh --stop-daemon"
}
...
Running this at the command line I get an annoying warning,
since apparently the daemon command calls runuser which
assumes the user has a home directory (which in my setup
is not true):
runuser: warning: cannot change directory to /home/galaxy: No such
file or directory
This is probably nothing Galaxy specific, probably a sign that
I'm not doing this in the recommended CentOS/RedHat way.
If I switch to a galaxy user with a home directory, this issue
should go away.
Peter