[Bio-linux-dev] bio-linux v. debian-med in 10.04, 12.04

[Tim Booth]

Hi Will,

This is what I'm working on just now.  By the time I'm done, all the
bio-linux-* packages will either contain a piece of software for which
there is no regular Debian package (eg. bio-linux-fastqc) or they will
be a wrapper package that depends on the regular package (eg.
bio-linux-arb).

The wrapper packages may include things specific to Bio-Linux - like
extra documentation or example files or scripts or icons.  Debian policy
is you only package what is in the upstream release.  Bio-Linux policy
is to bung in other stuff if it looks useful.  Users may choose what
they prefer.

Also, the versions of packages on BL may be more recent than on Precise
(for example I've just rebuilt BLAST+ 2.2.26) but I've done it by
updating the regular ncbi-blast+ package rather than updating the
redundant bio-linux-blast-plus package.  Also some packages are not in
Precise because they are still in Debian Experimental but I've brought
them into Bio-Linux.  Work in progress is here:

https://launchpad.net/~nebc/+archive/bio-linux

BL7 will pull packages directly from this repo.

I've just done "qiime" so I'm getting there.  Some packages aren't
behaving themselves and it's taking a while.

Cheers,

TIM

On Wed, 2012-08-15 at 17:00 +0100, William Spooner wrote:
> There are various packages in the set of cloud-bio-linux sources that are bio-linux v. debian-med duplicates on the Lucid (10.04) distro. A good example would be emboss. 
> 
> 1. Has anyone created a mapping?
> 2. Should I prefer the debian-med packages over the bio-linux packages?
> 3. Will the dups still be there for Precise (12.04)?
> 
> Thanks in advance,
> 
> Will
> 
> ---
> William Spooner           http://eaglegenomics.com
> M:07779-663045 E:william.spooner at eaglegenomics.com 
> 
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-- 
Tim Booth <tbooth at ceh.ac.uk>
NERC Environmental Bioinformatics Centre 

Centre for Ecology and Hydrology
Maclean Bldg, Benson Lane
Crowmarsh Gifford
Wallingford, England
OX10 8BB 

http://nebc.nerc.ac.uk
+44 1491 69 2705
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