From a.travis at abdn.ac.uk  Sat Oct  3 11:34:12 2009
From: a.travis at abdn.ac.uk (Tony Travis)
Date: Sat, 03 Oct 2009 16:34:12 +0100
Subject: [Bio-linux-dev] You've been tagged
Message-ID: <4AC76EF4.6090306@abdn.ac.uk>

Hello,

Just thought you might to see this favourable snippet:

http://koolinus.wordpress.com/2009/10/03/bio-linux-ubuntu-and-bioinformatics/

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



From a.travis at abdn.ac.uk  Wed Oct 14 06:58:09 2009
From: a.travis at abdn.ac.uk (Tony Travis)
Date: Wed, 14 Oct 2009 11:58:09 +0100
Subject: [Bio-linux-dev] blast2
Message-ID: <4AD5AEC1.5090407@abdn.ac.uk>

The updated blast2 now used in the NEBC mirror of blast2 from Debian sid 
breaks Bio-Linux under Ubuntu 6.06, and prevent 'unattended' upgrades.

This can be resolved by 'pinning' blast2 in /etc/apt/preferences:

Package: blast2
Pin: release a=dapper
Pin-Priority: 1001

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



From tbooth at ceh.ac.uk  Wed Oct 14 07:36:14 2009
From: tbooth at ceh.ac.uk (Tim Booth)
Date: Wed, 14 Oct 2009 12:36:14 +0100
Subject: [Bio-linux-dev] blast2
In-Reply-To: <4AD5AEC1.5090407@abdn.ac.uk>
References: <4AD5AEC1.5090407@abdn.ac.uk>
Message-ID: <1255520174.13568.1761.camel@barsukas>

Hi Tony,

Thanks for reporting this.  The fact that the old package even worked on
6.06 was really more down to accident than design.  I'm not sure what
version of Blast comes with Dapper, but it must be pretty old.  If Blast
is important to your users, a better option might be to pin
bio-linux-blast at version 2.20 or else to grab the software straight
from the NCBI and install it into /usr/local, removing bio-linux-blast
entirely.

On a related subject, though we're still a bit bogged down here in the
logistics of moving to Wallingford, we are working on a plan to be ready
for the upcoming 10.04 LTS.  We'll keep this list posted.

Cheers,

TIM

On Wed, 2009-10-14 at 11:58 +0100, Tony Travis wrote:
> The updated blast2 now used in the NEBC mirror of blast2 from Debian sid 
> breaks Bio-Linux under Ubuntu 6.06, and prevent 'unattended' upgrades.
> 
> This can be resolved by 'pinning' blast2 in /etc/apt/preferences:
> 
> Package: blast2
> Pin: release a=dapper
> Pin-Priority: 1001
> 
> Bye,
> 
>    Tony.
-- 
Tim Booth <tbooth at ceh.ac.uk>
NERC Environmental Bioinformatics Centre 
at CEH Oxford
+44 1865 281 975