[Bio-linux-dev] bio-linux-galaxy or galaxy-server

[William Spooner]

Thanks Tim,

I cannot believe how much drift there is in the sysV init system between distros! Anyway, fwiw, here is my attempt at a no-frills startup script for galaxy on Ubuntu;

---
#!/bin/sh 
# 
# Galaxy init script written by William Spooner, adapted from original by Michael Rusch 
# 

### BEGIN INIT INFO 
# Provides:                     galaxy 
# Required-Start:               $local_fs $remote_fs $network 
# X-UnitedLinux-Should-Start:   postgresql 
# Required-Stop:                $local_fs $remote_fs $network 
# X-UnitedLinux-Should-Stop: 
# Default-Start:                3 5 
# Default-Stop:                 0 1 2 6 
# Short-Description:            Galaxy daemon 
# Description:                  Start the Galaxy daemon 
### END INIT INFO 

GALAXY_DIR="/usr/local/galaxy"
GALAXY_RUN="$GALAXY_DIR/run.sh" 
GALAXY_LOG="$GALAXY_DIR/paster.log"
GALAXY_LCK="/tmp/galaxy.run.lock"
GALAXY_USER="galaxy" 
RETVAL=0

case "$1" in 
    start) 
        echo -n "Starting galaxy..." 
        sudo -u $GALAXY_USER env HOME=$GALAXY_DIR $GALAXY_RUN --log-file=$GALAXY_LOG --daemon 
	RETVAL=$?
        echo
        [ $RETVAL = 0 ] && touch $GALAXY_LCK
        return $RETVAL
        ;; 
    stop) 
        echo -n "Stopping galaxy..." 
        sudo -u $GALAXY_USER env HOME=$GALAXY_DIR $GALAXY_RUN --stop-daemon 
	RETVAL=$?
	echo
	[ $RETVAL = 0 ] && rm -f $GALAXY_LCK
        ;; 
    restart) 
        $0 stop 
        $0 start 
        ;; 
    *) 
        echo "Usage: $0 start|stop|restart" 
        exit 1 
esac 
---




> 
On 9 Jul 2012, at 16:02, Tim Booth wrote:

> Hi Will,
> 
> Sorry, the redundant bio-linux-* packages have now been cleaned off the
> server.  All the packages (aside from the OpenOffice one which has
> nothing to do with this) are ours.  If you want to try Galaxy with all
> the default package dependencies, install "galaxy-server-all".
> 
> These have not yet been officially announced because, while complete,
> there is still a bit more testing to do before I'm happy and we can
> co-ordinate an announcement with our collaborators in Manchester.
> 
> Note that you'll get a warning about two missing packages - we can't put
> these on the main server due to licensing restrictions.
> 
> And yes, I'd be interested in the startup script.  I need to review the
> latest packaging guidelines but I think we'll need separate startup
> scripts for Ubuntu and Debian if this is to work on both.  
> There's some
> way to go before the Galaxy packages (at least the core) could make it
> to Debian-Med, though, as I've employed some very nasty hacks to get
> them building!
> 
> Cheers,
> 
> TIM
> 
>> $ aptitude search galaxy
>> p   bio-linux-galaxy-all  - A web-based analysis environment with third party dependencies                                
>> p   bio-linux-galaxy-core - A web-based analysis environment                                                              
>> p   bio-linux-galaxy-dependencies - Third party dependencies for Galaxy (a web-based analysis tool)                               
>> p   galaxy-server - A web-based analysis environment                                                              
>> p   galaxy-server-all - Galaxy server with all recommended tools                                                      
>> p   galaxy-server-test - Test and demo data for Galaxy server                                                          
>> p   openoffice.org-style-galaxy - office productivity suite -- Galaxy (Default) symbol style        
>> 
>> So galaxy seems to be packaged twice, once by bio-linux, and once
>> elsewhere. Tim and Soon Gweon are the maintainers in bot cases. So -
>> should I be using bio-linux-galaxy or galaxy-server?
>> 
>> Tim - I also have a debian service-compatible init.d startup script
>> for galaxy if you're interested. Similar to the
>> current /etc/init/galaxy.conf, but with greater functionality.
>> 
>> Best,
>> 
>> Will
>> 
>> ---
>> William Spooner           http://eaglegenomics.com
>> M:07779-663045 E:william.spooner at eaglegenomics.com 
>> 
>> _______________________________________________
>> Bio-Linux-dev mailing list
>> Bio-Linux-dev at nebclists.nerc.ac.uk
>> http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux-dev
> 
> -- 
> Tim Booth <tbooth at ceh.ac.uk>
> NERC Environmental Bioinformatics Centre 
> 
> Centre for Ecology and Hydrology
> Maclean Bldg, Benson Lane
> Crowmarsh Gifford
> Wallingford, England
> OX10 8BB 
> 
> http://nebc.nerc.ac.uk
> +44 1491 69 2705
> 
> -- 
> This message (and any attachments) is for the recipient only. NERC
> is subject to the Freedom of Information Act 2000 and the contents
> of this email and any reply you make may be disclosed by NERC unless
> it is exempt from release under the Act. Any material supplied to
> NERC may be stored in an electronic records management system.
> 
> _______________________________________________
> Bio-Linux-dev mailing list
> Bio-Linux-dev at nebclists.nerc.ac.uk
> http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux-dev

---
William Spooner           http://eaglegenomics.com
M:07779-663045 E:william.spooner at eaglegenomics.com