Re: Worth packaging bio_assembly_refinement?
Thanks to all for the helpful comments. We'll look into bundling it with the circlator source package until the necessary components officially get merged into circlator. regards Afif -- Afif Elghraoui | عفيف الغراوي http://afif.ghraoui.name
Re: Worth packaging bio_assembly_refinement?
Hi Thank you for looking into this. Bio_assembly_refinement does not need to be a standalone package. Nishadi On 08/03/2016 08:36, "Martin Hunt" wrote: >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 >>was¹t sure what part of it is really needed, since it¹s description >>sounded a bit similar to Circlator itself. I didn¹t have the time yet to >>look into it in more detail yet. >> I have cc¹d 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.
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.
Re: Worth packaging bio_assembly_refinement?
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
Re: Worth packaging bio_assembly_refinement?
On الإثنين 7 آذار 2016 21:48, Afif Elghraoui wrote: > Hi, Sascha, > 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/. Thanks and regards Afif -- Afif Elghraoui | عفيف الغراوي http://afif.ghraoui.name
Worth packaging bio_assembly_refinement?
Hi, Sascha, 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? Thanks and regards Afif -- Afif Elghraoui | عفيف الغراوي http://afif.ghraoui.name
