From tbooth at ceh.ac.uk  Mon Jul  9 10:11:06 2012
From: tbooth at ceh.ac.uk (Tim Booth)
Date: Mon, 09 Jul 2012 15:11:06 +0100
Subject: [Bio-linux-dev] Bio-Linux dev
Message-ID: <1341843066.2700.224.camel@balisaur>

Hi Will,

Thanks for joining the bio-linux-dev mailing list.

It's a bit of a ghost ship just now, but there will be things happening
on this once I'm back from BOSC!  I promise!  

I'm very interested to ask you about installing/promoting your EnsEMBL
stuff on BL.  And also to see if you at Eagle have any interest in
Galaxy, as that's to be our big new supported feature on BL7.  EnsEMBL +
Galaxy in-a-can with timely updates has to be a good thing, right?

Cheers,

TIM

-- 
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.



From william.spooner at eaglegenomics.com  Mon Jul  9 10:17:06 2012
From: william.spooner at eaglegenomics.com (William Spooner)
Date: Mon, 9 Jul 2012 15:17:06 +0100
Subject: [Bio-linux-dev] bio-linux-galaxy or galaxy-server
Message-ID: <638244CB-6AC9-4949-8D22-52DBEEFAC2BB@eaglegenomics.com>

Dear BL-ers,

If I look for galaxy packages on a fresh CloudBioLinux instance, I see;

$ 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 



From william.spooner at eaglegenomics.com  Mon Jul  9 10:38:08 2012
From: william.spooner at eaglegenomics.com (William Spooner)
Date: Mon, 9 Jul 2012 15:38:08 +0100
Subject: [Bio-linux-dev] Bio-Linux dev
In-Reply-To: <1341843066.2700.224.camel@balisaur>
References: <1341843066.2700.224.camel@balisaur>
Message-ID: <5BBBE317-BB32-4814-82DF-68347E2F64AF@eaglegenomics.com>

Hi Tim,

We've let the Ensembl packaging drift a little, I'm ashamed to say. This will be rekindled pretty soon though, and I would love to work with BL to make sure it's distributed and publicised.

I'm busy writing opscode chef deployment scripts for galaxy using BL as the base platform. It seems to install much faster from apt than Galaxy's bitbucket.

Best,

Will

On 9 Jul 2012, at 15:11, Tim Booth wrote:

> Hi Will,
> 
> Thanks for joining the bio-linux-dev mailing list.
> 
> It's a bit of a ghost ship just now, but there will be things happening
> on this once I'm back from BOSC!  I promise!  
> 
> I'm very interested to ask you about installing/promoting your EnsEMBL
> stuff on BL.  And also to see if you at Eagle have any interest in
> Galaxy, as that's to be our big new supported feature on BL7.  EnsEMBL +
> Galaxy in-a-can with timely updates has to be a good thing, right?
> 
> Cheers,
> 
> TIM
> 
> -- 
> 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.
> 

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



From tbooth at ceh.ac.uk  Mon Jul  9 11:02:58 2012
From: tbooth at ceh.ac.uk (Tim Booth)
Date: Mon, 09 Jul 2012 16:02:58 +0100
Subject: [Bio-linux-dev] bio-linux-galaxy or galaxy-server
In-Reply-To: <638244CB-6AC9-4949-8D22-52DBEEFAC2BB@eaglegenomics.com>
References: <638244CB-6AC9-4949-8D22-52DBEEFAC2BB@eaglegenomics.com>
Message-ID: <1341846178.2700.256.camel@balisaur>

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.



From tbooth at ceh.ac.uk  Mon Jul  9 11:15:15 2012
From: tbooth at ceh.ac.uk (Tim Booth)
Date: Mon, 09 Jul 2012 16:15:15 +0100
Subject: [Bio-linux-dev] bio-linux-galaxy or galaxy-server
In-Reply-To: <1341846178.2700.256.camel@balisaur>
References: <638244CB-6AC9-4949-8D22-52DBEEFAC2BB@eaglegenomics.com>
	<1341846178.2700.256.camel@balisaur>
Message-ID: <1341846915.2700.263.camel@balisaur>

Oh, and as this is the developer list, I should mention the source
packages and latest development commits are all available:

https://launchpad.net/~nebc/+archive/galaxy

Right now we've pushed all the binary packages to the main package
server in advance of announcing them, so you don't get anything newer by
using the development PPA.  

We're also hoping to get our packages synced into the debian-med SVN but
this isn't feasible until we ditch Ubuntu 10.04 as there are now so many
incompatibilities between the legacy and contemporary source packages.

Cheers,

TIM

On Mon, 2012-07-09 at 16:02 +0100, 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
> 

-- 
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.



From william.spooner at eaglegenomics.com  Mon Jul  9 11:46:03 2012
From: william.spooner at eaglegenomics.com (William Spooner)
Date: Mon, 9 Jul 2012 16:46:03 +0100
Subject: [Bio-linux-dev] bio-linux-galaxy or galaxy-server
In-Reply-To: <1341846178.2700.256.camel@balisaur>
References: <638244CB-6AC9-4949-8D22-52DBEEFAC2BB@eaglegenomics.com>
	<1341846178.2700.256.camel@balisaur>
Message-ID: <AE1800D5-8558-44F6-92F5-4E31105D7B04@eaglegenomics.com>

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 



From ajt at minke.ukfsn.org  Mon Jul  9 11:55:02 2012
From: ajt at minke.ukfsn.org (Tony Travis)
Date: Mon, 09 Jul 2012 16:55:02 +0100
Subject: [Bio-linux-dev] bio-linux-galaxy or galaxy-server
In-Reply-To: <AE1800D5-8558-44F6-92F5-4E31105D7B04@eaglegenomics.com>
References: <638244CB-6AC9-4949-8D22-52DBEEFAC2BB@eaglegenomics.com>
	<1341846178.2700.256.camel@balisaur>
	<AE1800D5-8558-44F6-92F5-4E31105D7B04@eaglegenomics.com>
Message-ID: <4FFAFED6.802@minke.ukfsn.org>

On 09/07/12 16:46, William Spooner wrote:
> 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;

Hi, Will.

Ubuntu has now adopted "upstart" instead of the SysV init system!

Not all startup scripts have been migrated, but the ones that have are 
actually symlinks:

   /etc/init.d/name -> /lib/init/upstart-job

Which reads the relevant name.conf in:

   /etc/init/name.conf

HTH,

   Tony.





From william.spooner at eaglegenomics.com  Mon Jul  9 12:12:38 2012
From: william.spooner at eaglegenomics.com (William Spooner)
Date: Mon, 9 Jul 2012 17:12:38 +0100
Subject: [Bio-linux-dev] bio-linux-galaxy or galaxy-server
In-Reply-To: <4FFAFED6.802@minke.ukfsn.org>
References: <638244CB-6AC9-4949-8D22-52DBEEFAC2BB@eaglegenomics.com>
	<1341846178.2700.256.camel@balisaur>
	<AE1800D5-8558-44F6-92F5-4E31105D7B04@eaglegenomics.com>
	<4FFAFED6.802@minke.ukfsn.org>
Message-ID: <322BC462-2F2E-4060-AAF4-A4CE5565C867@eaglegenomics.com>


On 9 Jul 2012, at 16:55, Tony Travis wrote:

> On 09/07/12 16:46, William Spooner wrote:
>> 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;
> 
> Hi, Will.
> 
> Ubuntu has now adopted "upstart" instead of the SysV init system!
> 
> Not all startup scripts have been migrated, but the ones that have are actually symlinks:
> 
>  /etc/init.d/name -> /lib/init/upstart-job
> 
> Which reads the relevant name.conf in:
> 
>  /etc/init/name.conf
> 
> HTH,
> 
>  Tony.

Thanks Tony,

The first example name.conf I looked at was ufw, which simply calls '/lib/ufw/ufw-init start'. So you probably could use the same galaxy-init for both Deb and Ubuntu, you'd just need to call them differently. Oh what merry japes!

Will



From ajt at minke.ukfsn.org  Mon Jul  9 12:39:08 2012
From: ajt at minke.ukfsn.org (Tony Travis)
Date: Mon, 09 Jul 2012 17:39:08 +0100
Subject: [Bio-linux-dev] bio-linux-galaxy or galaxy-server
In-Reply-To: <322BC462-2F2E-4060-AAF4-A4CE5565C867@eaglegenomics.com>
References: <638244CB-6AC9-4949-8D22-52DBEEFAC2BB@eaglegenomics.com>
	<1341846178.2700.256.camel@balisaur>
	<AE1800D5-8558-44F6-92F5-4E31105D7B04@eaglegenomics.com>
	<4FFAFED6.802@minke.ukfsn.org>
	<322BC462-2F2E-4060-AAF4-A4CE5565C867@eaglegenomics.com>
Message-ID: <4FFB092C.3030009@minke.ukfsn.org>

On 09/07/12 17:12, William Spooner wrote:
> [...]
> The first example name.conf I looked at was ufw, which simply calls
> '/lib/ufw/ufw-init start'. So you probably could use the same
> galaxy-init for both Deb and Ubuntu, you'd just need to call them
> differently. Oh what merry japes!

Hi, Will.

There is a bit more to "upstart" than how the scripts are invoked.

The basic idea is that the /etc/init/*.conf files describe the desired 
state of the system - "upstart" then runs 'jobs' according to events, 
not static SysV (K)ill and (S)tart rules for different init levels:

   http://upstart.ubuntu.com/

I like it ;-)

Bye,

   Tony.




From william.spooner at eaglegenomics.com  Mon Jul  9 12:44:29 2012
From: william.spooner at eaglegenomics.com (William Spooner)
Date: Mon, 9 Jul 2012 17:44:29 +0100
Subject: [Bio-linux-dev] bio-linux-galaxy or galaxy-server
In-Reply-To: <4FFB092C.3030009@minke.ukfsn.org>
References: <638244CB-6AC9-4949-8D22-52DBEEFAC2BB@eaglegenomics.com>
	<1341846178.2700.256.camel@balisaur>
	<AE1800D5-8558-44F6-92F5-4E31105D7B04@eaglegenomics.com>
	<4FFAFED6.802@minke.ukfsn.org>
	<322BC462-2F2E-4060-AAF4-A4CE5565C867@eaglegenomics.com>
	<4FFB092C.3030009@minke.ukfsn.org>
Message-ID: <0FFEFF6A-D874-4872-87F0-76D5741481E4@eaglegenomics.com>


On 9 Jul 2012, at 17:39, Tony Travis wrote:

> On 09/07/12 17:12, William Spooner wrote:
>> [...]
>> The first example name.conf I looked at was ufw, which simply calls
>> '/lib/ufw/ufw-init start'. So you probably could use the same
>> galaxy-init for both Deb and Ubuntu, you'd just need to call them
>> differently. Oh what merry japes!
> 
> Hi, Will.
> 
> There is a bit more to "upstart" than how the scripts are invoked.
> 
> The basic idea is that the /etc/init/*.conf files describe the desired state of the system - "upstart" then runs 'jobs' according to events, not static SysV (K)ill and (S)tart rules for different init levels:
> 
>  http://upstart.ubuntu.com/
> 
> I like it ;-)

Yes - seems an improvement over SysV. Maybe it will become universally adopted ;)




> 
> Bye,
> 
>  Tony.
> 
> 
> _______________________________________________
> 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 



From william.spooner at eaglegenomics.com  Tue Jul 10 10:34:46 2012
From: william.spooner at eaglegenomics.com (William Spooner)
Date: Tue, 10 Jul 2012 15:34:46 +0100
Subject: [Bio-linux-dev] bio-linux-galaxy or galaxy-server
In-Reply-To: <1341846178.2700.256.camel@balisaur>
References: <638244CB-6AC9-4949-8D22-52DBEEFAC2BB@eaglegenomics.com>
	<1341846178.2700.256.camel@balisaur>
Message-ID: <29BB7CA2-B19A-47EE-8D95-EB72821C1C7C@eaglegenomics.com>

Hi Tim,

I'm rolling my own BioLinux by adding the repositories to sources.list. When installing galaxy on 10.04 I get the following;

---
$ sudo apt-get install galaxy-server-all
Reading package lists... Done
Building dependency tree       
Reading state information... Done
Some packages could not be installed. This may mean that you have
requested an impossible situation or if you are using the unstable
distribution that some required packages have not yet been created
or been moved out of Incoming.
The following information may help to resolve the situation:

The following packages have unmet dependencies:
  galaxy-server-all: Depends: python-rpy but it is not going to be installed
                     Recommends: ucsc-tools-non-free but it is not installable
                     Recommends: laj but it is not installable
E: Broken packages
---

The error is because galaxy needs a very specific version of python-rpy (due to a cascade to r-base-core) that I can get as follows;

$ sudo apt-get install python-rpy=1.0.3-17lucid1

galaxy-server-all now installs correctly.

Best,

will


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 



From tbooth at ceh.ac.uk  Mon Jul 16 12:57:44 2012
From: tbooth at ceh.ac.uk (Tim Booth)
Date: Mon, 16 Jul 2012 17:57:44 +0100
Subject: [Bio-linux-dev] bio-linux-galaxy or galaxy-server
In-Reply-To: <29BB7CA2-B19A-47EE-8D95-EB72821C1C7C@eaglegenomics.com>
References: <638244CB-6AC9-4949-8D22-52DBEEFAC2BB@eaglegenomics.com>
	<1341846178.2700.256.camel@balisaur>
	<29BB7CA2-B19A-47EE-8D95-EB72821C1C7C@eaglegenomics.com>
Message-ID: <1342457864.3973.52.camel@balisaur>

Hi Will,

> The following packages have unmet dependencies:
>   galaxy-server-all: Depends: python-rpy but it is not going to be installed
>                      Recommends: ucsc-tools-non-free but it is not installable
>                      Recommends: laj but it is not installable
> E: Broken packages
> ---
> 
> The error is because galaxy needs a very specific version of
> python-rpy (due to a cascade to r-base-core) that I can get as
> follows;
> 
> $ sudo apt-get install python-rpy=1.0.3-17lucid1

Ah yes, the version of python-rpy in our repository is compiled to work
with the latest version of r-base-core from CRAN, and APT isn't smart
enough (without hinting) to know that it needs to pick the version off
the Ubuntu server rather then the NEBC server.

Two possible fixes for this:

1) Get CRAN to make a working version of python-rpy so I don't need to
roll my own

2) Teach Galaxy to use python-rpy2 instead

I'll look into both of these.

Cheers,

TIM

-- 
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.



From william.spooner at eaglegenomics.com  Mon Jul 16 13:02:23 2012
From: william.spooner at eaglegenomics.com (William Spooner)
Date: Mon, 16 Jul 2012 18:02:23 +0100
Subject: [Bio-linux-dev] bio-linux-galaxy or galaxy-server
In-Reply-To: <1342457864.3973.52.camel@balisaur>
References: <638244CB-6AC9-4949-8D22-52DBEEFAC2BB@eaglegenomics.com>
	<1341846178.2700.256.camel@balisaur>
	<29BB7CA2-B19A-47EE-8D95-EB72821C1C7C@eaglegenomics.com>
	<1342457864.3973.52.camel@balisaur>
Message-ID: <436C0543-1EA4-4D39-8584-131786DCE2A5@eaglegenomics.com>


On 16 Jul 2012, at 17:57, Tim Booth wrote:

> Hi Will,
> 
>> The following packages have unmet dependencies:
>>  galaxy-server-all: Depends: python-rpy but it is not going to be installed
>>                     Recommends: ucsc-tools-non-free but it is not installable
>>                     Recommends: laj but it is not installable
>> E: Broken packages
>> ---
>> 
>> The error is because galaxy needs a very specific version of
>> python-rpy (due to a cascade to r-base-core) that I can get as
>> follows;
>> 
>> $ sudo apt-get install python-rpy=1.0.3-17lucid1
> 
> Ah yes, the version of python-rpy in our repository is compiled to work
> with the latest version of r-base-core from CRAN, and APT isn't smart
> enough (without hinting) to know that it needs to pick the version off
> the Ubuntu server rather then the NEBC server.
> 
> Two possible fixes for this:
> 
> 1) Get CRAN to make a working version of python-rpy so I don't need to
> roll my own
> 
> 2) Teach Galaxy to use python-rpy2 instead

Circular dependency hell? Don't envy you?

Will


> 
> I'll look into both of these.
> 
> Cheers,
> 
> TIM
> 
> -- 
> 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 



From william.spooner at eaglegenomics.com  Tue Jul 10 09:00:05 2012
From: william.spooner at eaglegenomics.com (William Spooner)
Date: Tue, 10 Jul 2012 14:00:05 +0100
Subject: [Bio-linux-dev] Key or keyserver for
	http://nebc.nox.ac.uk/bio-linux/
Message-ID: <745C4153-A328-4564-AA2B-51E3630260B3@eaglegenomics.com>

Hi,

I'm getting the following error from apt-get update after adding the bio-linux repository;

W: GPG error: http://nebc.nox.ac.uk unstable Release: The following signatures couldn't be verified because the public key is not available: NO_PUBKEY B1A598E8128B92BD

The problem is that the apt-get failure is breaking my workflow. Is there any way to add the bio-linux key to apt before running update, e.g. using something akin to one of the following;

 # curl -s http://archive.cloudera.com/debian/archive.key | apt-key add -
 # apt-key adv --keyserver keyserver.ubuntu.com --recv 7F0CEB10

Thanks,

Will

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



From tbooth at ceh.ac.uk  Thu Jul 19 09:30:04 2012
From: tbooth at ceh.ac.uk (Tim Booth)
Date: Thu, 19 Jul 2012 14:30:04 +0100
Subject: [Bio-linux-dev] Key or keyserver for
 http://nebc.nox.ac.uk/bio-linux/
In-Reply-To: <745C4153-A328-4564-AA2B-51E3630260B3@eaglegenomics.com>
References: <745C4153-A328-4564-AA2B-51E3630260B3@eaglegenomics.com>
Message-ID: <1342704604.3973.259.camel@balisaur>

Hi Will,

(Did you really send this on the 10th, or is it just that your system
date is out on your PC?)

Anyway, the key has been on the Ubuntu keyserver for some time, so I'm
not sure why you are having problems retrieving it.  I just tried myself
and it worked fine.  What error do you get exactly?

Cheers,

TIM

On Tue, 2012-07-10 at 14:00 +0100, William Spooner wrote:
> Hi,
> 
> I'm getting the following error from apt-get update after adding the
> bio-linux repository;
> 
> W: GPG error: http://nebc.nox.ac.uk unstable Release: The following
> signatures couldn't be verified because the public key is not
> available: NO_PUBKEY B1A598E8128B92BD
> 
> The problem is that the apt-get failure is breaking my workflow. Is
> there any way to add the bio-linux key to apt before running update,
> e.g. using something akin to one of the following;
> 
>  # curl -s http://archive.cloudera.com/debian/archive.key | apt-key
> add -
>  # apt-key adv --keyserver keyserver.ubuntu.com --recv 7F0CEB10
> 
> Thanks,
> 
> 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.



From william.spooner at eaglegenomics.com  Thu Jul 19 09:42:49 2012
From: william.spooner at eaglegenomics.com (William Spooner)
Date: Thu, 19 Jul 2012 14:42:49 +0100
Subject: [Bio-linux-dev] Key or keyserver for
	http://nebc.nox.ac.uk/bio-linux/
In-Reply-To: <1342704604.3973.259.camel@balisaur>
References: <745C4153-A328-4564-AA2B-51E3630260B3@eaglegenomics.com>
	<1342704604.3973.259.camel@balisaur>
Message-ID: <3A6AF420-A5BD-4D3F-8C01-FAA5B801FA60@eaglegenomics.com>

Thanks Tim,
Yup - mail was sent on 10th ;)

Well - it now works beautifuly!
  apt-key adv --keyserver keyserver.ubuntu.com --recv B1A598E8128B92BD

No idea what was up on the 10th. Just one of those things? 

Best,

Will

On 19 Jul 2012, at 14:30, Tim Booth wrote:

> Hi Will,
> 
> (Did you really send this on the 10th, or is it just that your system
> date is out on your PC?)
> 
> Anyway, the key has been on the Ubuntu keyserver for some time, so I'm
> not sure why you are having problems retrieving it.  I just tried myself
> and it worked fine.  What error do you get exactly?
> 
> Cheers,
> 
> TIM
> 
> On Tue, 2012-07-10 at 14:00 +0100, William Spooner wrote:
>> Hi,
>> 
>> I'm getting the following error from apt-get update after adding the
>> bio-linux repository;
>> 
>> W: GPG error: http://nebc.nox.ac.uk unstable Release: The following
>> signatures couldn't be verified because the public key is not
>> available: NO_PUBKEY B1A598E8128B92BD
>> 
>> The problem is that the apt-get failure is breaking my workflow. Is
>> there any way to add the bio-linux key to apt before running update,
>> e.g. using something akin to one of the following;
>> 
>> # curl -s http://archive.cloudera.com/debian/archive.key | apt-key
>> add -
>> # apt-key adv --keyserver keyserver.ubuntu.com --recv 7F0CEB10
>> 
>> Thanks,
>> 
>> 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