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

[Tony Travis]

When I used Bio-Linux 4, based on Debian Sarge, to create 'biobuntu' I 
simply installed the NEBC deb packages under Ubuntu 6.06 LTS (Dapper).

   http://nbx1.nugo.org/biobuntu

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.

For example, to compare packages on my local machine with the current 
Bio-Linux reference list:

   dpkg-dsel localhost bio-linux-6.0.24-desktop

Or, to compare my machine with a remote one:

   dpkg-dsel localhost manager at better.managed.host

I used this for quite a while on our NBX (NuGO Black Box) project and it 
has proved quite useful. However, I suspect that there might be a 
simpler way of doing this using Debian tools I don't know about ;-)

Attached is a tarball that creates a 'selection' file that can be used 
to set the APT selections for a 'dselect-upgrade', or as a reference 
file for my "dpkg-dsel" script. My main purpose in posting this is to 
ask if anyone has a better way of doing this, but it might also be 
useful if you want to check what packages are added/removed from your 
Bio-Linux installation by comparing your selections with a reference.

The lists are derived from the 'manifest' files that describe which 
packages are installed in the 'casper' squashfs' on the Ununtu or 
Bio-Linux 'live' install CD/DVD. One thing to note is that the desktop 
'manifest' of Bio-Linux is identical to the full manifest for the 'live' 
install DVD and this causes some packages that should not be present on 
the Bio-Linux 'desktop' being installed. I've removed these packages 
from the 'desktop' manifest by comparison with Ubuntu.

One reason why I've done this is to install a 'server' version of 
Bio-Linux by setting the extra Bio-Linux package selections in an Ubuntu 
server instance, and then upgrading it to Bio-Linux.

Please tell me gently if there is an easier way of doing it ;-)

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
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