[med-svn] [sap] 01/10: Take over information from tasks file into machine parseable code

[Andreas Tille]

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commit ec21345d2efdc9fdcd42c26c4d1e373f4f253c62
Author: Andreas Tille <tille at debian.org>
Date:   Mon May 28 15:32:50 2012 +0000

    Take over information from tasks file into machine parseable code
---
 debian/changelog |  5 +++++
 debian/compat    |  1 +
 debian/control   | 36 ++++++++++++++++++++++++++++++++++++
 debian/copyright | 10 ++++++++++
 debian/rules     |  6 ++++++
 debian/upstream  | 20 ++++++++++++++++++++
 6 files changed, 78 insertions(+)

diff --git a/debian/changelog b/debian/changelog
new file mode 100644
index 0000000..a6aba20
--- /dev/null
+++ b/debian/changelog
@@ -0,0 +1,5 @@
+sap (1.1.1-1) unstable; urgency=low
+
+  * Initial release
+
+ -- Andreas Tille <tille at debian.org>  Mon, 28 May 2012 17:14:53 +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..0b63901
--- /dev/null
+++ b/debian/control
@@ -0,0 +1,36 @@
+Source: sap
+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://mathbio.nimr.mrc.ac.uk/wiki/Software#SAP
+Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/sap/trunk/
+Vcs-Svn: svn://svn.debian.org/debian-med/trunk/packages/sap/trunk/
+
+Package: sap
+Architecture: any
+Depends: ${shlibs:Depends}, ${misc:Depends}
+Enhances: t-coffee
+Description:  Pairwise protein structure alignment via double dynamic programming
+ In contrast to DNA, proteins exhibit an apparently unlimited variety of
+ structure. This is a necessary requirement of the vast array of
+ differing functions that they perform in the maintainance of life,
+ again, in contrast to the relatively static archival function of DNA.
+ Not only do we observe a bewildering variety of form but even within a
+ common structure, there is variation in the lengths and orientation
+ substructures. Such variation is both a reflection on the very long time
+ periods over which some structures have diverged and also a consequence
+ of the fact that proteins cannot be completely rigid bodies but must
+ have flexibility to accommodate the structural changes that are almost
+ always necessary for them to perform their functions. These aspects make
+ comparing structure and finding structural similarity over long
+ divergence times very difficult. Indeed, computationally, the problem of
+ recognizing similarity is one of three-dimensional pattern recognition,
+ which is a notoriously difficult problem for computers to perform. In
+ this chapter, guidance is provided on the use of a flexible structure
+ comparison method that overcomes many of the problems of comparing
+ protein structures that may exhibit only weak similarity.
+
diff --git a/debian/copyright b/debian/copyright
new file mode 100644
index 0000000..83d9ee2
--- /dev/null
+++ b/debian/copyright
@@ -0,0 +1,10 @@
+Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Source: http://mathbio.nimr.mrc.ac.uk/download/SAP/sap-1.1.1.tar.gz
+
+Files: *
+Copyright: © 2008-2010 Willie Taylor <wtaylor at nimr.mrc.ac.uk>
+License: GPL-v3
+
+Files: debian/*
+Copyright: © 2012 Andreas Tille <tille at debian.org>
+License: GPL-v3
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..98a61ea
--- /dev/null
+++ b/debian/upstream
@@ -0,0 +1,20 @@
+Reference:
+ - Author: William R. Taylor
+   Title: Protein Structure Comparison Using SAP
+   Booktitle: "Protein Structure Prediction: Methods and Protocols"
+   Year: 2000
+   Volume: 143
+   Pages: 19-32
+   DOI: 10.1385/1-59259-368-2:19
+   URL: http://www.springerprotocols.com/Abstract/doi/10.1385/1-59259-368-2:19
+ - Author: William R. Taylor
+   Title: Protein structure comparison using iterated double dynamic programming
+   Journal: Protein Science
+   Year: 1999
+   Volume: 8
+   Number: 3
+   Pages: 654-65
+   DOI: 10.1110/ps.8.3.654
+   PMID: 10091668
+   URL: http://onlinelibrary.wiley.com/doi/10.1110/ps.8.3.654/abstract
+   eprint: http://onlinelibrary.wiley.com/doi/10.1110/ps.8.3.654/pdf

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