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

[Florent Angly]

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 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.
>
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