[med-svn] [fastml2] 02/02: Adapt Debian packaging

[Andreas Tille]

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tille pushed a commit to branch master
in repository fastml2.

commit 1771e2b0f89a4bdaa7e050af093f7a6eee20a05f
Author: Andreas Tille <tille at debian.org>
Date:   Mon Jun 22 13:23:50 2015 +0200

    Adapt Debian packaging
---
 debian/changelog         |  6 ++++++
 debian/control           | 29 +++++++++++++++++++++--------
 debian/rules             |  7 -------
 debian/source/format     |  1 +
 debian/upstream/metadata | 23 +++++++++++++++++++++++
 debian/watch             |  6 ++++++
 6 files changed, 57 insertions(+), 15 deletions(-)

diff --git a/debian/changelog b/debian/changelog
index 8aac9a5..e36cdf2 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,3 +1,9 @@
+fastml2 (2.0.3-1) UNRELEASED; urgency=low
+
+  * Initial Debian release (Closes: #<bug>)
+
+ -- Andreas Tille <tille at debian.org>  Mon, 22 Jun 2015 09:47:25 +0200
+
 fastml2 (2.2~trusty1) trusty; urgency=medium
 
   * Packaging tweaks
diff --git a/debian/control b/debian/control
index 90ec6ba..de7aa2b 100644
--- a/debian/control
+++ b/debian/control
@@ -1,13 +1,26 @@
 Source: fastml2
-Section: misc
-Priority: extra
-Maintainer: Aidan Delaney <aidan at ontologyengineering.org>
-Build-Depends: debhelper (>= 8.0.0), make
-Standards-Version: 3.9.4
-Vcs-Git: https://github.com/sanger-pathogens/fastml
+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),
+Standards-Version: 3.9.6
+Vcs-Browser: http://anonscm.debian.org/gitweb/?p=debian-med/fastml2.git
+Vcs-Git: git://anonscm.debian.org/debian-med/fastml2.git
+Homepage: http://fastml.tau.ac.il/source.html
 
 Package: fastml2
 Architecture: any
 Depends: ${shlibs:Depends}, ${misc:Depends}
-Description: Maximum likelihood reconstruction of ancestral amino-acid sequences.
-  A branch-and-bound algorithm for the inference of ancestral amino-acid sequences when the replacement rate varies among sites.
+Description: Maximum likelihood reconstruction of ancestral amino-acid sequences
+ A branch-and-bound algorithm for the inference of ancestral amino-acid
+ sequences when the replacement rate varies among sites.
+ .
+ FIXME:
+ .
+ This repository provides some additional functionality to fastml to allow it to
+ work with Gubbins. The original code is available from
+ http://fastml.tau.ac.il/source.html and should be your first port of call. To
+ modify the original code, or use parts of it for other purposes, permission
+ should be requested. Please contact Tal Pupko: talp at post.tau.ac.il
diff --git a/debian/rules b/debian/rules
index 63fc6d6..019047f 100755
--- a/debian/rules
+++ b/debian/rules
@@ -1,11 +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..3f5138f
--- /dev/null
+++ b/debian/upstream/metadata
@@ -0,0 +1,23 @@
+Reference:
+ - Author: Haim Ashkenazy and Osnat Penn and Adi Doron-Faigenboim and Ofir Cohen and Gina Cannarozzi and Oren Zomer and Tal Pupko
+   Title: "FastML: a web server for probabilistic reconstruction of ancestral sequences"
+   Journal: Nucleic Acids Research
+   Year: 2012
+   Volume: 40
+   Number: Web Server issue
+   Pages: W580-4
+   DOI: 10.1093/nar/gks498
+   PMID: 22661579
+   URL: http://nar.oxfordjournals.org/content/40/W1/W580
+   eprint: http://nar.oxfordjournals.org/content/40/W1/W580.full.pdf+html
+ - Author: Tal Pupko and Itsik Peer and Masami Hasegawa and Dan Graur and Nir Friedman
+   Title: A branch-and-bound algorithm for the inference of ancestral amino-acid sequences when the replacement rate varies among sites: Application to the evolution of five gene families
+   Journal: Bioinformatics
+   Year: 2002
+   Volume: 18
+   Number: 8
+   DOI: 10.1093/bioinformatics/18.8.1116
+   Pages: 1116-23
+   PMID: 12176835
+   URL: http://bioinformatics.oxfordjournals.org/content/18/8/1116.abstract
+   eprint: http://bioinformatics.oxfordjournals.org/content/18/8/1116.full.pdf+html
diff --git a/debian/watch b/debian/watch
new file mode 100644
index 0000000..8804550
--- /dev/null
+++ b/debian/watch
@@ -0,0 +1,6 @@
+version=3
+
+## FIXME: Does not detect latest version!!!
+
+opts="uversionmangle=s/^(\d\.\d)/$1./"
+ https://github.com/andrewjpage/fastml/releases .*/archive/v(\d[\d.-]+)\.(?:tar(?:\.gz|\.bz2)?|tgz)

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