[med-svn] r23449 - in trunk/packages/euler2/trunk/debian: . upstream

Mon Jan 2 15:29:52 UTC 2017

Author: tille
Date: 2017-01-02 15:29:50 +0000 (Mon, 02 Jan 2017)
New Revision: 23449

Added:
   trunk/packages/euler2/trunk/debian/upstream/
   trunk/packages/euler2/trunk/debian/upstream/metadata
Modified:
   trunk/packages/euler2/trunk/debian/changelog
   trunk/packages/euler2/trunk/debian/compat
   trunk/packages/euler2/trunk/debian/control
   trunk/packages/euler2/trunk/debian/copyright
   trunk/packages/euler2/trunk/debian/rules
Log:
Normalise packaging, add uptream metadata


Modified: trunk/packages/euler2/trunk/debian/changelog
===================================================================

--- trunk/packages/euler2/trunk/debian/changelog	2017-01-02 15:15:44 UTC (rev 23448)
+++ trunk/packages/euler2/trunk/debian/changelog	2017-01-02 15:29:50 UTC (rev 23449)
@@ -1,4 +1,4 @@
-euler2 (2.0-1) unstable; urgency=low
+euler2 (2.0-1) UNRELEASED; urgency=low
 
   * Initial release
 

Modified: trunk/packages/euler2/trunk/debian/compat
===================================================================
--- trunk/packages/euler2/trunk/debian/compat	2017-01-02 15:15:44 UTC (rev 23448)
+++ trunk/packages/euler2/trunk/debian/compat	2017-01-02 15:29:50 UTC (rev 23449)
@@ -1 +1 @@
-5
+10

Modified: trunk/packages/euler2/trunk/debian/control
===================================================================
--- trunk/packages/euler2/trunk/debian/control	2017-01-02 15:15:44 UTC (rev 23448)
+++ trunk/packages/euler2/trunk/debian/control	2017-01-02 15:29:50 UTC (rev 23449)
@@ -1,18 +1,28 @@
 Source: euler2
+Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+Uploaders: Andreas Tille <tille at debian.org>
 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: cdbs, debhelper, quilt
-Standards-Version: 3.8.0
+Build-Depends: debhelper (>= 10)
+Standards-Version: 3.9.8
+Vcs-Browser: https://anonscm.debian.org/viewvc/debian-med/trunk/packages/euler2/
+Vcs-Svn: svn://anonscm.debian.org/debian-med/trunk/packages/euler2/trunk/
 Homepage: http://nbcr.sdsc.edu/euler/document.htm
-Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/euler2/
-Vcs-Svn: svn://svn.debian.org/debian-med/trunk/packages/euler2/trunk/
 
 Package: euler2
 Architecture: any
 Section: science
-Depends: ${shlibs:Depends}, graphviz
-Description: short description
- long description
+Depends: ${shlibs:Depends},
+         graphviz
+Description: de novo repeat classification and fragment assembly
+ Repetitive sequences make up a significant fraction of almost any genome
+ and an important and still open question in bioinformatics is how to
+ represent all repeats in DNA sequences. We propose a radically new
+ approach to repeat classification that is motivated by the fundamental
+ topological notion of quotient spaces. A torus or Klein bottle are
+ examples of quotient spaces that can be obtained from a square by gluing
+ some points. Our new repeat classification algorithm is based on the
+ observation that the alignment-induced quotient space of a DNA sequence
+ compactly represents all sequence repeats. This observation leads to a
+ simple and efficient solution of the repeat classification problem as
+ well as new approaches to fragment assembly and multiple alignment.

Modified: trunk/packages/euler2/trunk/debian/copyright
===================================================================
--- trunk/packages/euler2/trunk/debian/copyright	2017-01-02 15:15:44 UTC (rev 23448)
+++ trunk/packages/euler2/trunk/debian/copyright	2017-01-02 15:29:50 UTC (rev 23449)
@@ -1,8 +1,9 @@
-X-Format-Specification: http://wiki.debian.org/Proposals/CopyrightFormat
-X-Debianized-By: Andreas Tille <tille at debian.org>
-X-Debinized-Date: Tue,  9 Dec 2008 14:19:29 +0100.
-X-Upstream-Author: Pavel A. Pevzner, Haixu Tang and Glenn Tesler
-X-Homepage: http://nbcr.sdsc.edu/euler/document.htm
+Formats: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Upstream-Contact: Pavel A. Pevzner <ppevzner at cs.ucsd.edu>,
+                  Haixu Tang<htang at cs.ucsd.edu>
+Source: https://git.wageningenur.nl/aflit001/tools/tree/master/aflit001/bin/euler2
+Comments: The source is just a code copy found in a different project.
+          The original source code seems to have vanished.
 
 Files: *
 Copyright: (C) 2001-2004 The Regents of the University of California.

Modified: trunk/packages/euler2/trunk/debian/rules
===================================================================
--- trunk/packages/euler2/trunk/debian/rules	2017-01-02 15:15:44 UTC (rev 23448)
+++ trunk/packages/euler2/trunk/debian/rules	2017-01-02 15:29:50 UTC (rev 23449)
@@ -1,15 +1,4 @@
 #!/usr/bin/make -f
-# debian/rules for euler2 using cdbs
-# Andreas Tille <tille at debian.org>, GPL
 
-include /usr/share/cdbs/1/rules/patchsys-quilt.mk
-include /usr/share/cdbs/1/rules/debhelper.mk
-include /usr/share/cdbs/1/class/makefile.mk
-
-DEB_OPT_FLAG += -Iinc/
-
-get-orig-source:
-	echo "You have to gegister to obtain the upstream source"
-
-clean::
-	rm -f `grep -v -e '^*\.pl' -e '^debian/' debian/install | sed 's?[[:space:]]\+usr/[a-z0-9/]\+??'`
+%:
+	dh $@

Added: trunk/packages/euler2/trunk/debian/upstream/metadata
===================================================================
--- trunk/packages/euler2/trunk/debian/upstream/metadata	                        (rev 0)
+++ trunk/packages/euler2/trunk/debian/upstream/metadata	2017-01-02 15:29:50 UTC (rev 23449)
@@ -0,0 +1,8 @@
+Reference:
+  Author: Pavel A. Pevzner and Haixu Tang and Glenn Tesler
+  Title: "De novo repeat classification and fragment assembly"
+  Journal: "RECOMB '04 Proceedings of the eighth annual international conference on Resaerch in computational molecular biology"
+  Year: 2004
+  Pages: 213-222
+  DOI: 10.1145/974614.974643
+  URL: https://dl.acm.org/citation.cfm?doid=974614.974643


