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

[William Spooner]

Thanks Tim, that's fantastic.

In which case I will use the bio-linux-* packages wherever possible. 

Should I presume that everything in http://nebc.nerc.ac.uk/bio-linux/dists/unstable/bio-linux will work on Lucid? How do you separate the packages in BL6 from those in BL7?

Did bio-linux ever package any of the tools that are now in precise/universe? Namely bioconductor, vcftools and bedtools?

Best,

Will

On 15 Aug 2012, at 17:58, Tim Booth wrote:

> 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 
> 
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> 
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---
William Spooner           http://eaglegenomics.com
M:07779-663045 E:william.spooner at eaglegenomics.com