[med-svn] [ngila] 01/13: Inject information from task file and WNPP bug

[Andreas Tille]

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tille pushed a commit to branch master
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commit a67342c8684ae5f00d30c2d551710106c7ea9146
Author: Andreas Tille <tille at debian.org>
Date:   Sun May 27 07:01:02 2012 +0000

    Inject information from task file and WNPP bug
---
 debian/changelog |  5 +++++
 debian/compat    |  1 +
 debian/control   | 31 +++++++++++++++++++++++++++++++
 debian/copyright | 10 ++++++++++
 debian/rules     |  6 ++++++
 debian/upstream  | 12 ++++++++++++
 6 files changed, 65 insertions(+)

diff --git a/debian/changelog b/debian/changelog
new file mode 100644
index 0000000..5b1eaee
--- /dev/null
+++ b/debian/changelog
@@ -0,0 +1,5 @@
+ngila (1.3-1) unstable; urgency=low
+
+  * Initial release (Closes: #439996)
+
+ -- Andreas Tille <tille at debian.org>  Sun, 27 May 2012 08:49:50 +0200
diff --git a/debian/compat b/debian/compat
new file mode 100644
index 0000000..ec63514
--- /dev/null
+++ b/debian/compat
@@ -0,0 +1 @@
+9
diff --git a/debian/control b/debian/control
new file mode 100644
index 0000000..60d3109
--- /dev/null
+++ b/debian/control
@@ -0,0 +1,31 @@
+Source: ngila
+Section: science
+Priority: optional
+Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+DM-Upload-Allowed: yes
+Uploaders: Andreas Tille <tille at debian.org>
+Build-Depends: debhelper (>= 9)
+Standards-Version: 3.9.3
+Homepage: http://scit.us/projects/ngila/
+Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/ngila/trunk/
+Vcs-Svn: svn://svn.debian.org/debian-med/trunk/packages/ngila/trunk/
+
+Package: ngila
+Architecture: any
+Depends: ${shlibs:Depends}, ${misc:Depends}
+Description: global pairwise alignments with logarithmic and affine gap costs
+ Ngila is an application that will find the best alignment of a pair
+ of sequences using log-affine gap costs, which are the most
+ biologically realistic gap costs.
+ .
+ Ngila implements the Miller and Myers (1988) algorithm in order to
+ find a least costly global alignment of two sequences given homology
+ costs and a gap cost. Two versions of the algorithm are
+ included: holistic and divide-and-conquer. The former is faster but
+ the latter utilizes less memory. Ngila starts with the
+ divide-and-conquer method but switches to the holistic method for
+ subsequences smaller than a user-established threshold. This improves
+ its speed without substantially increasing memory requirements. Ngila
+ also allows users to assign costs to end gaps that are smaller than
+ costs for internal gaps. This is important for aligning using the
+ free-end-gap method.
diff --git a/debian/copyright b/debian/copyright
new file mode 100644
index 0000000..4bd03f2
--- /dev/null
+++ b/debian/copyright
@@ -0,0 +1,10 @@
+Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Source: http://scit.us/projects/ngila/downloads
+
+Files: *
+Copyright: © 2008-2011 Reed A. Cartwright <racartwright at rice.edu>
+License: GPLv3
+
+Files: debian/*
+Copyright: © 2012 Andreas Tille <tille at debian.org>
+License: GPLv3
diff --git a/debian/rules b/debian/rules
new file mode 100755
index 0000000..6055261
--- /dev/null
+++ b/debian/rules
@@ -0,0 +1,6 @@
+#!/usr/bin/make -f
+
+# DH_VERBOSE := 1
+
+%:
+	dh $@
diff --git a/debian/upstream b/debian/upstream
new file mode 100644
index 0000000..ab97e4a
--- /dev/null
+++ b/debian/upstream
@@ -0,0 +1,12 @@
+Reference:
+  Author: Reed A. Cartwright
+  Title: "Ngila: global pairwise alignments with logarithmic and affine gap costs"
+  Journal: Bioinformatics
+  Year: 2007
+  Volume: 23
+  Number: 11
+  Pages: 1427-1428
+  DOI: 10.1093/bioinformatics/btm095
+  PMID: 17387111
+  URL: http://bioinformatics.oxfordjournals.org/content/23/11/1427
+  eprint: http://bioinformatics.oxfordjournals.org/content/23/11/1427.full.pdf+html

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