[Bio-linux-dev] Fwd: Re: How to check Bio-Linux package selections

[Tony Travis]

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 écrit :
>>
>> 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.