From plessy at debian.org  Sun May  1 06:36:53 2011
From: plessy at debian.org (Charles Plessy)
Date: Sun, 1 May 2011 19:36:53 +0900
Subject: [Bio-linux-dev] How to check Bio-Linux package selections
In-Reply-To: <4DBA97D5.9060501@minke.ukfsn.org>
References: <4DBA97D5.9060501@minke.ukfsn.org>
Message-ID: <20110501103653.GA10180@merveille.plessy.net>

Le Fri, Apr 29, 2011 at 11:49:57AM +0100, Tony Travis a ?crit :
> 
> I wanted to make sure that 'biobuntu' was as close to Bio-Linux as
> possible, but based on Ubuntu instead of Debian. I wrote a script
> "dpkg-dsel" to compare the 'dselect' selections of two machines or to
> compare the current selections of one machine with a reference list of
> package selections obtained from the installation media.

Dear Tony,

comparing the output of ?dpkg --get-selections? will not only reflect the
difference of what the ?bio? pakcages need, but also the differences between
Debian and Ubuntu in general, plus the differences in the way they were
installed.

I feel that it would be simpler to rely on APT than on dpkg, by having a list
of packages that are required for your system to be a ?biobuntu?, and letting
APT pull everything else that is necessary.  That will also help you to upgrade
from one Ubuntu release to the others.

The list of packages can be a meta-package.  You could either write one from
scratch, or modify the Debian Med blends packages.  It would not be too
difficult to unbrand or rebrand them.

Have a nice day,

-- 
Charles Plessy
Debian Med packaging team,
http://www.debian.org/devel/debian-med
Tsurumi, Kanagawa, Japan


From a.travis at abdn.ac.uk  Tue May  3 06:46:58 2011
From: a.travis at abdn.ac.uk (Tony Travis)
Date: Tue, 03 May 2011 11:46:58 +0100
Subject: [Bio-linux-dev] Fwd: Re: How to check Bio-Linux package selections
Message-ID: <4DBFDD22.3070102@abdn.ac.uk>

Forwarded from debian-med:

-------- Original Message --------
Subject: Re: How to check Bio-Linux package selections
Resent-Date: Sun,  1 May 2011 19:04:03 +0000 (UTC)
Resent-From: debian-med at lists.debian.org
Date: Sun, 01 May 2011 20:03:42 +0100
From: Tony Travis <ajt at minke.ukfsn.org>
To: debian-med at lists.debian.org

On 01/05/11 11:36, Charles Plessy wrote:
> Le Fri, Apr 29, 2011 at 11:49:57AM +0100, Tony Travis a ?crit :
>>
>> I wanted to make sure that 'biobuntu' was as close to Bio-Linux as
>> possible, but based on Ubuntu instead of Debian. I wrote a script
>> "dpkg-dsel" to compare the 'dselect' selections of two machines or to
>> compare the current selections of one machine with a reference list of
>> package selections obtained from the installation media.
>
> Dear Tony,
>
> comparing the output of ?dpkg --get-selections? will not only reflect the
> difference of what the ?bio? pakcages need, but also the differences between
> Debian and Ubuntu in general, plus the differences in the way they were
> installed.

Hi, Charles.

It was only during the initial stages that I compared Debian (Sarge) and
Ubuntu (Dapper). Bio-Linux is based on Ubuntu 10.04 LTS, so I'm now
actually comparing an Ubuntu derivative (Bio-Linux) with Ubuntu.

> I feel that it would be simpler to rely on APT than on dpkg, by having a list
> of packages that are required for your system to be a ?biobuntu?, and letting
> APT pull everything else that is necessary.  That will also help you to upgrade
> from one Ubuntu release to the others.

I just use "dpkg" to set the selections, I then install them using:

   aptitude -f install

> The list of packages can be a meta-package.  You could either write one from
> scratch, or modify the Debian Med blends packages.  It would not be too
> difficult to unbrand or rebrand them.

Yes, I've thought of creating a meta-package - One thing that has
stopped from doing that me so far is not knowing how to create a package
dependency tree and how to prune off all the lower level dependencies
that could be installed automatically. A meta-package containing an
exhaustive list of all the required packages would not be an elegant
solution, would it?

However, an additional use of my "dpkg-dsel" script is to compare the
package 'selections' installed on different machines. I do this to track
the differences between various installations of Bio-Linux and Ubuntu as
well as comparing against a reference list of packages based on the
manifest of the 'squashfs' filesystem on the installation media.

Thanks for your helpful comments,

   Tony.



From florent.angly at gmail.com  Wed May  4 22:07:53 2011
From: florent.angly at gmail.com (Florent Angly)
Date: Thu, 05 May 2011 12:07:53 +1000
Subject: [Bio-linux-dev] Fwd: Re: How to check Bio-Linux package
	selections
In-Reply-To: <4DBFDD22.3070102@abdn.ac.uk>
References: <4DBFDD22.3070102@abdn.ac.uk>
Message-ID: <4DC20679.3050000@gmail.com>

Hi Tony,
Would this command not be easier?
     sudo apt-get install bio-linux*
Regards,
Florent

On 03/05/11 20:46, Tony Travis wrote:
> Forwarded from debian-med:
>
> -------- Original Message --------
> Subject: Re: How to check Bio-Linux package selections
> Resent-Date: Sun,  1 May 2011 19:04:03 +0000 (UTC)
> Resent-From: debian-med at lists.debian.org
> Date: Sun, 01 May 2011 20:03:42 +0100
> From: Tony Travis <ajt at minke.ukfsn.org>
> To: debian-med at lists.debian.org
>
> On 01/05/11 11:36, Charles Plessy wrote:
>> Le Fri, Apr 29, 2011 at 11:49:57AM +0100, Tony Travis a ?crit :
>>>
>>> I wanted to make sure that 'biobuntu' was as close to Bio-Linux as
>>> possible, but based on Ubuntu instead of Debian. I wrote a script
>>> "dpkg-dsel" to compare the 'dselect' selections of two machines or to
>>> compare the current selections of one machine with a reference list of
>>> package selections obtained from the installation media.
>>
>> Dear Tony,
>>
>> comparing the output of ?dpkg --get-selections? will not only reflect 
>> the
>> difference of what the ?bio? pakcages need, but also the differences 
>> between
>> Debian and Ubuntu in general, plus the differences in the way they were
>> installed.
>
> Hi, Charles.
>
> It was only during the initial stages that I compared Debian (Sarge) and
> Ubuntu (Dapper). Bio-Linux is based on Ubuntu 10.04 LTS, so I'm now
> actually comparing an Ubuntu derivative (Bio-Linux) with Ubuntu.
>
>> I feel that it would be simpler to rely on APT than on dpkg, by 
>> having a list
>> of packages that are required for your system to be a ?biobuntu?, and 
>> letting
>> APT pull everything else that is necessary.  That will also help you 
>> to upgrade
>> from one Ubuntu release to the others.
>
> I just use "dpkg" to set the selections, I then install them using:
>
>   aptitude -f install
>
>> The list of packages can be a meta-package.  You could either write 
>> one from
>> scratch, or modify the Debian Med blends packages.  It would not be too
>> difficult to unbrand or rebrand them.
>
> Yes, I've thought of creating a meta-package - One thing that has
> stopped from doing that me so far is not knowing how to create a package
> dependency tree and how to prune off all the lower level dependencies
> that could be installed automatically. A meta-package containing an
> exhaustive list of all the required packages would not be an elegant
> solution, would it?
>
> However, an additional use of my "dpkg-dsel" script is to compare the
> package 'selections' installed on different machines. I do this to track
> the differences between various installations of Bio-Linux and Ubuntu as
> well as comparing against a reference list of packages based on the
> manifest of the 'squashfs' filesystem on the installation media.
>
> Thanks for your helpful comments,
>
>   Tony.
>
> _______________________________________________
> Bio-Linux-dev mailing list
> Bio-Linux-dev at nebclists.nerc.ac.uk
> http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux-dev



From a.travis at abdn.ac.uk  Thu May  5 10:40:41 2011
From: a.travis at abdn.ac.uk (Tony Travis)
Date: Thu, 05 May 2011 15:40:41 +0100
Subject: [Bio-linux-dev] Fwd: Re: How to check Bio-Linux package
	selections
In-Reply-To: <4DC20679.3050000@gmail.com>
References: <4DBFDD22.3070102@abdn.ac.uk> <4DC20679.3050000@gmail.com>
Message-ID: <4DC2B6E9.8090907@abdn.ac.uk>

On 05/05/11 03:07, Florent Angly wrote:
> Hi Tony,
> Would this command not be easier?
>       sudo apt-get install bio-linux*

Hi, Florent.

Yes, in principle, I could install everything in Bio-Linux but this is 
most often not what is required and, in my case, I want to add some of 
the Bio-Linux packages to an existing server installation of Ubuntu 
10.04, or to compare which packages are already installed on several 
different servers including Bio-Linux packages and other packages not 
related to Bio-Linux.

Just out of interest I ran your command and you can see that things do 
not always turn out to be quite as simple as they first appear :-)

> sudo apt-get install bio-linux*
> Reading package lists... Done
> Building dependency tree
> Reading state information... Done
> Note, selecting bio-linux-sampledata for regex ?bio-linux*?
> [...]
> Note, selecting bio-linux-chimeraslayer for regex ?bio-linux*?
> 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.
>   bio-linux-emboss-kmenus: Depends: kaptain (<= 0.71-1.5) but it is not going to be installed
>   bio-linux-themes: Conflicts: bio-linux-themes-v5 but 1.2 is to be installed
>   bio-linux-themes-v5: Conflicts: bio-linux-themes but 6.1 is to be installed
>   bio-linux-yamap: Depends: bio-linux-glimmer but it is not installable
> E: Broken packages

Bye,

   Tony.
-- 
Dr. A.J.Travis, University of Aberdeen, Rowett Institute of Nutrition
and Health, Greenburn Road, Bucksburn, Aberdeen AB21 9SB, Scotland, UK
tel +44(0)1224 712751, fax +44(0)1224 716687, http://www.rowett.ac.uk
mailto:a.travis at abdn.ac.uk, http://bioinformatics.rri.sari.ac.uk


From tbooth at ceh.ac.uk  Mon May 23 07:06:59 2011
From: tbooth at ceh.ac.uk (Tim Booth)
Date: Mon, 23 May 2011 12:06:59 +0100
Subject: [Bio-linux-dev] New Bio-linux 6 image 6.0.25
Message-ID: <1306148819.3312.652.camel@barsukas>

Hi all,

This is just to record that I put an updated ISO onto the server.  Just
an updated version ready for the course we're teaching this week.  There
are still various outstanding wishlist items I've not been able to
tackle, but at least this version won't suffer from the CRAN key issue
and has the latest packages for HT sequence processing.

Also this image goes over the 2.2 GB file size limit so we are likely to
get reports form users that it isn't working.  I'm hoping to be able to
prune it a little and get a smaller 6.0.26 image out fairly soon.

Cheers,

TIM

Changelog for 6.0.25 (May 20th 2010)

        Fixed issue with CRAN signing key changing
        
        Updated all packages apart from kernel, Plymouth
        
        Added new Bio-Linux packages to default install:
        
                * bowtie
                * fastqc
                * jmotu
                * qiime
                * mothur
                * ampliconnoise
        
        Updated R packages in /usr/local/R/site-lib
        


-- 
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

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