9:55 a.m.
Hi all,
I'm trying to install Galaxy on CentOS, and doing things under my own
user account the basics look fine (sh setup.sh work, sh run.sh works,
and I can access the galaxy webpages on localhost).
I'm now trying to do this via a new Unix/Linux user account just for
Galaxy, as recommended here:
http://bitbucket.org/galaxy/galaxy-central/wiki/Config/ProductionServer
For security I have deliberately setup a "galaxy" user with no home
directory and with login disabled (based on the apache user):
sudo /usr/sbin/adduser -s /sbin/nologin -M -l -r -c "Galaxy" galaxy
I have downloaded Galaxy using hg, moved the directory to
/opt/galaxy-dist and made the new galaxy user the owner of
this folder and its contents. Then:
sudo -u galaxy sh setup.sh
That seems to work, next:
sudo -u galaxy sh run.sh
This fails as it tries to write to ~/.python-eggs (i.e. my home directory,
the galaxy user doesn't have a home directory), so based on the
error message's suggestion to set PYTHON_EGG_CACHE what
I have tied is editing run.sh to include the following line near the
start:
export PYTHON_EGG_CACHE="/opt/galaxy-dist/.python-eggs"
That seems to work, but is is a good idea? Do you instead
recommend giving the galaxy account a home directory, and
installing galaxy there? It would make setting environment
variables simpler...
Thanks,
Peter
1:09 p.m.
On Fri, Sep 3, 2010 at 10:55 AM, Peter <peter(a)maubp.freeserve.co.uk> wrote:
Hi all,
I'm trying to install Galaxy on CentOS, and doing things under my own
user account the basics look fine (sh setup.sh work, sh run.sh works,
and I can access the galaxy webpages on localhost).
I'm now trying to do this via a new Unix/Linux user account just for
Galaxy, as recommended here:
http://bitbucket.org/galaxy/galaxy-central/wiki/Config/ProductionServer
For security I have deliberately setup a "galaxy" user with no home
directory and with login disabled (based on the apache user) ...
That seems to work, but is is a good idea? Do you instead
recommend giving the galaxy account a home directory, and
installing galaxy there? It would make setting environment
variables simpler...
Reading galaxy-dist/contrib/galaxy.debian-init from James Casbon,
in his setup the galaxy user had a home directory and that is where
the galaxy files were kept. So at least some people do it that way.
Peter
3:20 p.m.
Peter wrote:
Hi all,
I'm trying to install Galaxy on CentOS, and doing things under my own
user account the basics look fine (sh setup.sh work, sh run.sh works,
and I can access the galaxy webpages on localhost).
I'm now trying to do this via a new Unix/Linux user account just for
Galaxy, as recommended here:
http://bitbucket.org/galaxy/galaxy-central/wiki/Config/ProductionServer
For security I have deliberately setup a "galaxy" user with no home
directory and with login disabled (based on the apache user):
sudo /usr/sbin/adduser -s /sbin/nologin -M -l -r -c "Galaxy" galaxy
I have downloaded Galaxy using hg, moved the directory to
/opt/galaxy-dist and made the new galaxy user the owner of
this folder and its contents. Then:
sudo -u galaxy sh setup.sh
That seems to work, next:
sudo -u galaxy sh run.sh
This fails as it tries to write to ~/.python-eggs (i.e. my home directory,
the galaxy user doesn't have a home directory), so based on the
error message's suggestion to set PYTHON_EGG_CACHE what
I have tied is editing run.sh to include the following line near the
start:
export PYTHON_EGG_CACHE="/opt/galaxy-dist/.python-eggs"
That seems to work, but is is a good idea? Do you instead
recommend giving the galaxy account a home directory, and
installing galaxy there? It would make setting environment
variables simpler...
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.
Please let us know if you encounter any more issues.
Thanks,
--nate
Thanks,
Peter
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3:51 p.m.
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
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Peter