[BioBrew Users] separate biobrew install?

Glen Otero gotero at linuxprophet.com
Thu Aug 28 16:01:17 EDT 2003

On Thursday, August 28, 2003, at 11:45  AM, Kip Lubliner wrote:

> hello,
> I am a newbie with all this BioBrew/Rocks stuff, and I'm not sure that 
> I understand how things are set up right now.  AFAIK, BioBrew 0.9 is 
> essentially Rocks 2.3.2 with additional bioinformatics packages.

This is true, for the most part.  One major difference is that I've 
dumped PBS for SGE. Technically, you would need to get a license for 
PBS to use it, so I won't include it. SGE is completely open source, 
freely redistributable, easier to use, and more robust IMHO.

> There are many other possible application areas, e.g. chemistry, 
> physics, etc.  Wouldn't it make more sense to have some sort of 
> 'package' structure that could be installed on the rocks front-end 
> directly after the regular Rocks install?  That way if someone wanted 
> to run bioinformatics programs and physics programs, they could just 
> install both 'packages'.  With the current situation, going to rocks 
> 3.0.0 would require Glen to release an updated BioBrew.

I actually intend to create other 'Brews' for computational chemistry, 
climate modeling, etc. A domain agnostic package structure makes sense 
for distribution of applications, and the Rocks folks are experimenting 
with this idea in their upcoming 3.0 release. So I may adopt that 
structure in the future. But for right now, since the bio packages that 
are included in BioBrew are just rpms that I've built, it's trivial 
(for me) to integrate them with a Rocks release to create BioBrew. I 
save people a lot of time and frustration by doing this. Installing 
BioBrew saves one the trouble of installing Rocks, and then downloading 
all the individual bio rpms, building and installing them on the 
Frontend, and then installing them on the compute nodes. I understand 
that if the cluster were to be used for more than just bio, like bio 
and physics, that doing a regular Rocks install and then grabbing the 
desired bio and physics packages would make the cluster a little more 
customizable. I have been kicking around the idea of making the 
individual bio SRPMS available in the biopackage repository so that 
folks can pick just the ones that they want. Is that something you 
would be interested in?


> Kip
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Glen Otero, Ph.D.
Linux Prophet

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