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Re: Worth packaging bio_assembly_refinement?



Hi,

From a Circlator point of view, I think it would be good to eventually have the relevant bits of bio_assembly_refinement put into Circlator. Circlator only uses one piece of functionality from bio_assembly_refinement.

I don't know what else bio_assembly_refinement is being used for, so can't comment on that as a stand-alone package.

Best,
Martin


On 08/03/2016 07:21, Sascha Steinbiss wrote:
Hi Afif,

first of all thanks for looking at Circlator, which was on my list as well :)

I'm looking into packaging Circlator, which depends on the Sanger
program bio_assembly_refinement. Looking into it, I'm wondering whether
this is a tool that will just get folded into circlator eventually. Do
you think it's worth packaging it separately?
I should add that the alternative would be to bundle it into the
circlator package as a multi-orig tarball. The question is better
rephrased as whether it's worth packaging bio_assembly_refinement
/separately/.
Yes, I noticed the dependency on bio_assembly_refinement as well and I was’t sure what part of it is really needed, since it’s description sounded a bit similar to Circlator itself. I didn’t have the time yet to look into it in more detail yet.
I have cc’d Martin Hunt, the Circlator author, and Nishadi de Silva, the bio_assembly_refinement author, on this email and they might be able to say more.

Many thanks,
Sascha


--
Dr. Martin Hunt
Senior Bioinformatician
Pathogen Informatics
Wellcome Trust Sanger Institute
Cambridge
UK

Tel: +44 (0)1223 834244



--
The Wellcome Trust Sanger Institute is operated by Genome Research Limited, a charity registered in England with number 1021457 and a company registered in England with number 2742969, whose registered office is 215 Euston Road, London, NW1 2BE.
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