On Fri, Sep 3, 2010 at 4:20 PM, Nate Coraor <nate@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