[Date Prev][Date Next] [Thread Prev][Thread Next] [Date Index] [Thread Index]

Bug#764232: marked as done (ITP: gubbins -- Gubbins (Genealogies Unbiased By recomBinations In Nucleotide Sequences) is an algorithm that iteratively identifies loci containing elevated densities of base substitutions while concurrently constructing a phylogeny based on the putative point mutations outside of these regions.)

Your message dated Sat, 05 Dec 2015 18:00:24 +0000
with message-id <E1a5H8C-0002RE-W9@franck.debian.org>
and subject line Bug#764232: fixed in gubbins 1.4.3-1
has caused the Debian Bug report #764232,
regarding ITP: gubbins -- Gubbins (Genealogies Unbiased By recomBinations In Nucleotide Sequences) is an algorithm that iteratively identifies loci containing elevated densities of base substitutions while concurrently constructing a phylogeny based on the putative point mutations outside of these regions.
to be marked as done.

This means that you claim that the problem has been dealt with.
If this is not the case it is now your responsibility to reopen the
Bug report if necessary, and/or fix the problem forthwith.

(NB: If you are a system administrator and have no idea what this
message is talking about, this may indicate a serious mail system
misconfiguration somewhere. Please contact owner@bugs.debian.org
immediately.)


-- 
764232: http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=764232
Debian Bug Tracking System
Contact owner@bugs.debian.org with problems
--- Begin Message --- 
Package: wnpp
Severity: wishlist
Owner: Jorge Soares <j.s.soares@gmail.com>

* Package name    : gubbins
  Version         : 0.6
  Upstream Author : Andrew Page <ap13@sanger.ac.uk> 
* URL             : https://github.com/sanger-pathogens/gubbins
* License         : GPL2
  Programming Lang: C, Python
  Description     : Gubbins (Genealogies Unbiased By recomBinations In Nucleotide Sequences) is an algorithm that iteratively identifies loci containing elevated densities of base substitutions while concurrently constructing a phylogeny based on the putative point mutations outside of these regions.

Since the introduction of high-throughput, second-generation DNA sequencing technologies,
there has been an enormous increase in the size of datasets being used for estimating bacterial population phylodynamics.
Although many phylogenetic techniques are scalable to hundreds of bacterial genomes,
methods which have been used for mitigating the effect of mechanisms of horizontal sequence
transfer on phylogenetic reconstructions cannot cope with these new datasets.
Gubbins (Genealogies Unbiased By recomBinations In Nucleotide Sequences) is an algorithm that
iteratively identifies loci containing elevated densities of base substitutions while
concurrently constructing a phylogeny based on the putative point mutations outside of these regions.
Simulations demonstrate the algorithm generates highly accurate reconstructions under
realistic models of short-term bacterial evolution, and can be run in only a few hours on alignments of hundreds of bacterial genome sequences.

--- End Message ---
--- Begin Message --- 
Source: gubbins
Source-Version: 1.4.3-1

We believe that the bug you reported is fixed in the latest version of
gubbins, which is due to be installed in the Debian FTP archive.

A summary of the changes between this version and the previous one is
attached.

Thank you for reporting the bug, which will now be closed.  If you
have further comments please address them to 764232@bugs.debian.org,
and the maintainer will reopen the bug report if appropriate.

Debian distribution maintenance software
pp.
Andreas Tille <tille@debian.org> (supplier of updated gubbins package)

(This message was generated automatically at their request; if you
believe that there is a problem with it please contact the archive
administrators by mailing ftpmaster@ftp-master.debian.org)


-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA256

Format: 1.8
Date: Mon, 30 Nov 2015 15:10:52 +0100
Source: gubbins
Binary: gubbins
Architecture: source amd64
Version: 1.4.3-1
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Changed-By: Andreas Tille <tille@debian.org>
Description:
 gubbins    - phylogenetic analysis of genome sequences
Closes: 764232 806726
Changes:
 gubbins (1.4.3-1) unstable; urgency=medium
 .
   * Initial Debian release (Closes: #764232, #806726)
Checksums-Sha1:
 7362455f7d6cccffa9e4a5e4d3895b80f58f33e7 2143 gubbins_1.4.3-1.dsc
 34f04da1cc198b03075fb92a40d0592bc106ffa7 322841 gubbins_1.4.3.orig.tar.gz
 eb10b37d2b51cb0f9f0687eedea00e0f6eb84a56 4920 gubbins_1.4.3-1.debian.tar.xz
 f401fad9692691f936f99330c99df9cbdba9dd46 50626 gubbins_1.4.3-1_amd64.deb
Checksums-Sha256:
 b0917c96212151da355e905c4b5fc8c4f8fbc6f51fc7873647cbf83ea4c85c92 2143 gubbins_1.4.3-1.dsc
 46bb389cea5df5ef2ac386d104e511fd96ae6389327cedc127a3cd4783c43a2a 322841 gubbins_1.4.3.orig.tar.gz
 50b0cc3bc918c7598a0605f043ddfef992913879bacb8f0ee2f155392033ce99 4920 gubbins_1.4.3-1.debian.tar.xz
 be04d04dbdb079698015d83ce18838ecb11ffcd56fd626ea35254bf00f8efcef 50626 gubbins_1.4.3-1_amd64.deb
Files:
 5eb9e995c15d4fa325be20c8749f9486 2143 science optional gubbins_1.4.3-1.dsc
 03b84e9d476c2f314a7af804db9c705e 322841 science optional gubbins_1.4.3.orig.tar.gz
 9f458968d894960d8d0e251e0a9e3ac3 4920 science optional gubbins_1.4.3-1.debian.tar.xz
 626e552e30be614323a84961a0eaf530 50626 science optional gubbins_1.4.3-1_amd64.deb

-----BEGIN PGP SIGNATURE-----
Version: GnuPG v1
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=jYpc
-----END PGP SIGNATURE-----

--- End Message ---
Reply to: