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Re: Clouds and NG sequencing

On Mon, Aug 09, 2010 at 07:15:15PM +0530, PRAKHAR gaur wrote:
> creating a Linux Distro is two fold. First I want to achieve a
> optimization in speed and efficiency with which a program runs. 
> Secondly its about the gain in knowledge and I am just curious to
> find out whether it can be done.
> The plan of work is to build a                                                                                                                                                                                  
> LFS system, and implement the modifications in it.                                                                                                                                                              
> Kernel                                                                                                                                                                                                          
> Modifications, Scheduler, File System(brtfs), a minimilistic                                                                                                                                                    
> approach, TWM as the default  desktop environment

For pure educational purpose this might be a reasonable thing to do.
However, if it is rather to do some tie saving by trying to optimise for
speed my experience tells me that you will never be able to trade of the
time you actually needed for the optimisation process against the time
you might later win because of the optimisation.  Finally it is up to
you to find this out yourself and I might be wrong in your specific case
but I personally doubt that this approach is efficient for a wider use
and so it is rather some accademical research you are doing (which is
perfectly fine for sure).

> Debian's
> package managent system as Debian-med is the most comprehensive 
> repository for Bioinformatics software.

Yes, that's what we are working for. ;-)
> I
> am currently learning to use dpkg and git for that. We have created a
> software package for Protein enggnering which I will share as soon as
> I can. 

This would be great - just ask for advise here in case of any trouble.
> As
> far as using Debian goes, I do use it as my Desktop OS. But the point
> is have a minimal system, which i feel can be achived only by
> compiling a Linux system from source. 

If you ask me, purging everything from a Debian machine which is not
needed and using a very minimalistic windowmanager brings you quite
there where you want to be.
> Also
> I my lab for the NGS work they use CentOS, because they feel that its
> more reliable(being a clone of RHEL). But I am trying to convert
> them, given that you guys already have Maq and BWA. 

IMHO the wide coverage of several interesting programs is the strength
of Debian Med.  DId you ever have shown your colleagues the page which
lists everything we have[1]?
> As
> mentioned above I am already doing that, getting my lab people to work
> on Debian and using it myself. I want to contribute by packaging  but still learning about the process. The
> Bioinfo Distro project is more for learning than anything else, its
> my first Linux related project. 

Thanks for the clarification


[1] http://debian-med.alioth.debian.org/tasks/bio


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