[med-svn] [gubbins] 02/02: Turn inofficial packaging into official packaging code

Andreas Tille tille at debian.org
Mon Jun 22 07:49:59 UTC 2015 

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tille pushed a commit to branch master
in repository gubbins.

commit b02735a52001f3bcee1a810ed7bcb70d3a5a7635
Author: Andreas Tille <tille at debian.org>
Date:   Mon Jun 22 09:59:12 2015 +0200

    Turn inofficial packaging into official packaging code
---
 debian/changelog         |  6 ++++++
 debian/control           | 37 ++++++++++++++++++++++++-------------
 debian/copyright         |  1 +
 debian/rules             |  6 ------
 debian/source/format     |  1 +
 debian/upstream/metadata | 12 ++++++++++++
 debian/watch             |  3 +++
 7 files changed, 47 insertions(+), 19 deletions(-)

diff --git a/debian/changelog b/debian/changelog
index 0de6f98..40a5259 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,3 +1,9 @@
+gubbins (1.3.4-1) UNRELEASED; urgency=low
+
+  * Initial Debian release (Closes: #<bug>)
+
+ -- Andreas Tille <tille at debian.org>  Mon, 22 Jun 2015 09:47:25 +0200
+
 gubbins (1.3.3~trusty1) trusty; urgency=low
 
   * Max window size arg bug
diff --git a/debian/control b/debian/control
index 2e0036c..7f8e4d9 100644
--- a/debian/control
+++ b/debian/control
@@ -1,17 +1,28 @@
 Source: gubbins
-Section: misc
-Priority: extra
-Maintainer: Aidan Delaney <a.j.delaney at brighton.ac.uk>
-# fastml, fasttree and raxml are required for the build in order to run the gubbins system tests.
-# There are a lot of build dependencies in order to run the system tests.
-Build-Depends: fastml2, fasttree, raxml, debhelper (>= 8.0.0), autotools-dev, python-setuptools, zlib1g-dev, check, python-biopython, python-reportlab, python-nose, pkg-config
-Standards-Version: 3.9.4
-Vcs-Git: https://github.com/andrewjpage/gubbins.git
-Vcs-Browser: https://github.com/andrewjpage/gubbins
+Section: science
+Priority: optional
+Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+Uploaders: Andreas Tille <tille at debian.org>,
+           Aidan Delaney <a.j.delaney at brighton.ac.uk>
+Build-Depends: debhelper (>= 9),
+               fastml2, fasttree, raxml, autotools-dev, python-setuptools, zlib1g-dev, check, python-biopython, python-reportlab, python-nose, pkg-config
+Standards-Version: 3.9.6
+Vcs-Browser: http://anonscm.debian.org/gitweb/?p=debian-med/gubbins.git
+Vcs-Git: git://anonscm.debian.org/debian-med/gubbins.git
+Homepage: https://sanger-pathogens.github.io/gubbins/
 
 Package: gubbins
-Architecture: amd64
-Recommends: raxml
-Depends: fastml2, fasttree, python-biopython, python-reportlab, python-nose, ${shlibs:Depends}, ${misc:Depends}
+Architecture: any
+Depends: ${shlibs:Depends}, ${misc:Depends}, fastml2, fasttree, python-biopython, python-reportlab, python-nose
 Description: Phylogenetic analysis of genome sequences
-  Gubbins supports rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences.
+ Gubbins supports rapid phylogenetic analysis of large samples of
+ recombinant bacterial whole genome sequences.
+ .
+ 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.
diff --git a/debian/copyright b/debian/copyright
index 9ad8745..6e80d2e 100644
--- a/debian/copyright
+++ b/debian/copyright
@@ -7,6 +7,7 @@ Copyright: 2012-2014 Nicholas Croucher <n.croucher at imperial.ac.uk>
            2012-2014 Aidan Delaney <a.j.delaney at brighton.ac.uk>
            2012-2014 Simon Harris <sh16 at sanger.ac.uk>
            2012-2014 Andrew J. Page <ap13 at sanger.ac.uk>
+License: GPL-2.0+
 
 License: GPL-2.0+
  This package is free software; you can redistribute it and/or modify
diff --git a/debian/rules b/debian/rules
index 312e24d..eac6ee4 100755
--- a/debian/rules
+++ b/debian/rules
@@ -1,10 +1,4 @@
 #!/usr/bin/make -f
-# -*- makefile -*-
-# Sample debian/rules that uses debhelper.
-# This file was originally written by Joey Hess and Craig Small.
-# As a special exception, when this file is copied by dh-make into a
-# dh-make output file, you may use that output file without restriction.
-# This special exception was added by Craig Small in version 0.37 of dh-make.
 
 # Uncomment this to turn on verbose mode.
 #export DH_VERBOSE=1
diff --git a/debian/source/format b/debian/source/format
new file mode 100644
index 0000000..163aaf8
--- /dev/null
+++ b/debian/source/format
@@ -0,0 +1 @@
+3.0 (quilt)
diff --git a/debian/upstream/metadata b/debian/upstream/metadata
new file mode 100644
index 0000000..b281b44
--- /dev/null
+++ b/debian/upstream/metadata
@@ -0,0 +1,12 @@
+Reference:
+  Author: Nicholas J. Croucher and Andrew J. Page and Thomas R. Connor and Aidan J. Delaney and Jacqueline A. Keane and Stephen D. Bentley and Julian Parkhill and Simon R. Harris
+  Title: Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins
+  Journal: Nucleic Acids Research
+  Year: 2014
+  Volume: 43
+  Number: 3
+  Pages: e15
+  DOI: 10.1093/nar/gku1196
+  PMID: 25414349
+  URL: http://nar.oxfordjournals.org/content/43/3/e15
+  eprint: http://nar.oxfordjournals.org/content/43/3/e15.full.pdf+html
diff --git a/debian/watch b/debian/watch
new file mode 100644
index 0000000..54f39c3
--- /dev/null
+++ b/debian/watch
@@ -0,0 +1,3 @@
+version=3
+
+https://github.com/sanger-pathogens/gubbins/releases .*/archive/v(\d[\d.-]+)\.(?:tar(?:\.gz|\.bz2)?|tgz)

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