[med-svn] r2564 - in trunk/packages: . seqan seqan/trunk seqan/trunk/debian

Wed Oct 1 07:44:19 UTC 2008

Author: sonne
Date: 2008-10-01 07:44:19 +0000 (Wed, 01 Oct 2008)
New Revision: 2564

Added:
   trunk/packages/seqan/
   trunk/packages/seqan/branches/
   trunk/packages/seqan/build-area/
   trunk/packages/seqan/tags/
   trunk/packages/seqan/trunk/
   trunk/packages/seqan/trunk/debian/
   trunk/packages/seqan/trunk/debian/changelog
   trunk/packages/seqan/trunk/debian/compat
   trunk/packages/seqan/trunk/debian/control
   trunk/packages/seqan/trunk/debian/copyright
   trunk/packages/seqan/trunk/debian/orig-tar.sh
   trunk/packages/seqan/trunk/debian/rules
   trunk/packages/seqan/trunk/debian/watch
Log:
import seqan

Added: trunk/packages/seqan/trunk/debian/changelog
===================================================================

--- trunk/packages/seqan/trunk/debian/changelog	                        (rev 0)
+++ trunk/packages/seqan/trunk/debian/changelog	2008-10-01 07:44:19 UTC (rev 2564)
@@ -0,0 +1,5 @@
+seqan (1.1-1) unstable; urgency=low
+
+  * Initial Release  (Closes: #487361)
+
+ -- Soeren Sonnenburg <debian at nn7.de>  Fri, 23 May 2008 16:09:47 +0200

Added: trunk/packages/seqan/trunk/debian/compat
===================================================================
--- trunk/packages/seqan/trunk/debian/compat	                        (rev 0)
+++ trunk/packages/seqan/trunk/debian/compat	2008-10-01 07:44:19 UTC (rev 2564)
@@ -0,0 +1 @@
+5

Added: trunk/packages/seqan/trunk/debian/control
===================================================================
--- trunk/packages/seqan/trunk/debian/control	                        (rev 0)
+++ trunk/packages/seqan/trunk/debian/control	2008-10-01 07:44:19 UTC (rev 2564)
@@ -0,0 +1,23 @@
+Source: seqan
+Section: science
+Priority: extra
+Maintainer: Debian-Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+Uploaders: Soeren Sonnenburg <sonne at debian.org>
+Build-Depends: cdbs, debhelper (>= 5)
+Standards-Version: 3.8.0
+Homepage: http://www.seqan.de/
+Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/seqan/?rev=0&sc=0
+Vcs-Svn: svn://svn.debian.org/svn/debian-med/trunk/packages/seqan/trunk/
+
+Package: seqan0-dev
+Section: libdevel
+Architecture: all
+Depends: ${shlibs:Depends}, ${misc:Depends}
+Description: A C++ template library for the analysis of sequences.
+ SeqAn is a C++ template library of efficient algorithms and data
+ structures for the analysis of sequences with the focus on
+ biological data. This library applies a unique generic design that
+ guarantees high performance, generality, extensibility, and
+ integration with other libraries. SeqAn is easy to use and
+ simplifies the development of new software tools with a minimal loss
+ of performance.

Added: trunk/packages/seqan/trunk/debian/copyright
===================================================================
--- trunk/packages/seqan/trunk/debian/copyright	                        (rev 0)
+++ trunk/packages/seqan/trunk/debian/copyright	2008-10-01 07:44:19 UTC (rev 2564)
@@ -0,0 +1,35 @@
+This package was debianized by by Soeren Sonnenburg <debian at nn7.de>.
+
+It was downloaded from http://www.seqan.de .
+
+The upstream authors are
+
+Andreas Döring <doering at inf.fu-berlin.de>
+David Weese <weese at inf.fu-berlin.de>
+Tobias Rausch <rausch at inf.fu-berlin.de>
+Stephan Aiche <aiche at inf.fu-berlin.de>
+Anne-Katrin Emde <emde at inf.fu-berlin.de>
+Carsten Kemena <kemena at inf.fu-berlin.de>
+Konrad Ludwig Moritz Rudolph <krudolph at inf.fu-berlin.de>
+
+The file index/index_sa_lss.h is Copyright 1999, N. Jesper Larsson <jesper at cs.lth.se>
+
+ This software may be used freely for any purpose. However, when distributed,
+ the original source must be clearly stated, and, when the source code is
+ distributed, the copyright notice must be retained and any alterations in
+ the code must be clearly marked. No warranty is given regarding the quality
+ of this software.*/
+
+
+The files
+ chaining/skip_list_base.h
+ chaining/skip_base_element.h
+ chaining/skip_list_impl.h
+ chaining/skip_list_dynamic.h
+ chaining/skip_element.h
+ chaining/skip_list.h
+ chaining/skip_list_iterator.h
+ chaining/skip_pool_alloc.h
+are Copyright 2006, Hendrik Woehrle 
+
+All rights reserved. NON-FREE - ASK AUTHORS!!!

Added: trunk/packages/seqan/trunk/debian/orig-tar.sh
===================================================================
--- trunk/packages/seqan/trunk/debian/orig-tar.sh	                        (rev 0)
+++ trunk/packages/seqan/trunk/debian/orig-tar.sh	2008-10-01 07:44:19 UTC (rev 2564)
@@ -0,0 +1,19 @@
+#!/bin/sh
+
+SEQANDIR=seqan-$2
+SEQANFILE=seqan-${2}.orig.tar.gz
+# called by uscan with '--upstream-version' <version> <file>
+mkdir $SEQANDIR
+unzip $3 -d $SEQANDIR
+tar czf $SEQANFILE $SEQANDIR
+rm -rf $SEQANDIR
+rm -f $3
+
+# move to directory 'tarballs'
+if [ -r .svn/deb-layout ]; then
+  . .svn/deb-layout
+  mv $SEQANFILE $origDir
+  echo "moved $SEQANFILE to $origDir"
+fi
+
+exit 0


Property changes on: trunk/packages/seqan/trunk/debian/orig-tar.sh
___________________________________________________________________
Name: svn:executable
   + *

Added: trunk/packages/seqan/trunk/debian/rules
===================================================================
--- trunk/packages/seqan/trunk/debian/rules	                        (rev 0)
+++ trunk/packages/seqan/trunk/debian/rules	2008-10-01 07:44:19 UTC (rev 2564)
@@ -0,0 +1,27 @@
+#!/usr/bin/make -f
+
+include /usr/share/cdbs/1/rules/debhelper.mk
+include /usr/share/cdbs/1/class/autotools.mk
+include /usr/share/cdbs/1/rules/patchsys-quilt.mk
+
+LDFLAGS += -lCoinUtils
+DEB_CONFIGURE_EXTRA_FLAGS += --enable-static CPPFLAGS=-I/usr/include/coin
+
+build/libclp-doc:: debian/stamp-build-libclp-doc
+debian/stamp-build-libclp-doc:
+	doxygen doxydoc/doxygen.conf
+	touch $@
+
+install/libclp-doc:: debian/stamp-install-libclp-doc
+debian/stamp-install-libclp-doc:
+	mkdir -p $(CURDIR)/debian/libclp-doc/usr/share/doc/libclp-doc/html
+	cd doxydoc/html && cp *.html *.png *.gif *.css $(CURDIR)/debian/libclp-doc/usr/share/doc/libclp-doc/html/
+	touch $@
+
+get-orig-source:
+	-uscan --rename --upstream-version 0
+	@echo successfully retrieved upstream tarball
+
+clean::
+	$(RM) -r debian/stamp-*
+


Property changes on: trunk/packages/seqan/trunk/debian/rules
___________________________________________________________________
Name: svn:executable
   + *

Added: trunk/packages/seqan/trunk/debian/watch
===================================================================
--- trunk/packages/seqan/trunk/debian/watch	                        (rev 0)
+++ trunk/packages/seqan/trunk/debian/watch	2008-10-01 07:44:19 UTC (rev 2564)
@@ -0,0 +1,6 @@
+version=3
+http://www.seqan.de/downloads/library/index.php \
+http://www.seqan.de/downloads/library/seqan-release-([\d\.]+)/download.html \
+		 debian debian/orig-tar.sh
+
+


