[Bio-Linux] AMD64 packages

[Tony Travis]

Luca Venturini wrote:
> Dear Tony,
>                    thank you for your quick answer. I had already seen 
> the biobuntu project page some time ago, but the blueprint there seemed 
> to indicate that the project had stopped with the release of the 
> Ubuntu-base BioLinux 5.0. Glad to read it is not so. In particular, the 
> possibility of a Biobuntu PPA is quite interesting, especially for 
> porting this software to 64 bit machines too. I look forward from 
> hearing news about this possibility.

Hello, Luca.

Development of 'biobuntu' did stop when Bio-Linux 5.0 was released, but 
I attended a meeting between NuGO (European Nutrigenomics Organisation), 
NTC (Dutch Toxicogenomics Consortium) and NEBC in Oxford last month to 
discuss collaboration on core features of a Linux-based bioinformatics 
workstation or server that we can customise for our respective users.

One possibility that we discussed was opening up Bio-Linux 'core' 
development to the Ubuntu developer community, via the blueprints and 
PPA. My 'biobuntu' blueprint could be a starting point for this, but I 
also want to develop it for clustering instances via Kerrighed/XtreemOS.

Please subscribe to my blueprint if you're interested.

> For now, however, do you have perchance any advice in installing this 
> software on a 64 bit system? In some months I will probably have to 
> switch from 32 bit to 64 (I plan on a huge upgrade on RAM), so I was 
> looking around for a smooth transition also in this area.
> Thank you for your kind attention.

You could use a 32-bit chroot to run a Bio-Linux userland under a 64-bit 
kernel. I've thought of doing this myself, but I've not actually tried 
it yet. NuGO currently has 31 NBX Opteron servers, mostly running 32-bit 
'biobuntu', but we are upgrading them to "NuGO-Linux" a Bio-Linux 5.0 
derivative customised for NuGO. If you're intererested, you can download 
the latest 'alpha' version of "NuGO-Linux" from:

   http://nbx1.nugo.org/biobuntu

I'm creating USB sticks from this, but we encountered problems using 
ext2 filesystems on out USB sticks created using bio-linux-usb-maker.

If you burn the nugo-linux-20090910.iso to DVD and try to create a USB 
stick using the hardy backport of Ubuntu "usb-creator" that is installed 
on it, you need to make a symbolic link to the CD device e.g.:

   ln -s /dev/scd0 cdrom.iso

This is because "usb-creator" doesn't detect the CD/DVD when running in 
a 'live' session: Something that bio-linux-usb-maker does do very well!

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/~ajt