[med-svn] r12136 - in trunk/packages: . zalign zalign/trunk zalign/trunk/debian zalign/trunk/debian/source

Mon Aug 27 13:40:37 UTC 2012

Author: moeller
Date: 2012-08-27 13:40:37 +0000 (Mon, 27 Aug 2012)
New Revision: 12136

Added:
   trunk/packages/zalign/
   trunk/packages/zalign/trunk/
   trunk/packages/zalign/trunk/debian/
   trunk/packages/zalign/trunk/debian/README.Debian
   trunk/packages/zalign/trunk/debian/changelog
   trunk/packages/zalign/trunk/debian/compat
   trunk/packages/zalign/trunk/debian/control
   trunk/packages/zalign/trunk/debian/copyright
   trunk/packages/zalign/trunk/debian/docs
   trunk/packages/zalign/trunk/debian/rules
   trunk/packages/zalign/trunk/debian/source/
   trunk/packages/zalign/trunk/debian/source/format
   trunk/packages/zalign/trunk/debian/watch
Log:
Sometimes one is surprised about packages not found in our distribution. ZAlign is such.


Added: trunk/packages/zalign/trunk/debian/README.Debian
===================================================================

--- trunk/packages/zalign/trunk/debian/README.Debian	                        (rev 0)
+++ trunk/packages/zalign/trunk/debian/README.Debian	2012-08-27 13:40:37 UTC (rev 12136)
@@ -0,0 +1,7 @@
+zalign for Debian
+-----------------
+
+ZAlign was only packaged for some imminent local need and seeks 
+a maintainer truly caring about it.
+
+ -- Steffen Moeller <moeller at debian.org>  Mon, 27 Aug 2012 15:14:15 +0200

Added: trunk/packages/zalign/trunk/debian/changelog
===================================================================
--- trunk/packages/zalign/trunk/debian/changelog	                        (rev 0)
+++ trunk/packages/zalign/trunk/debian/changelog	2012-08-27 13:40:37 UTC (rev 12136)
@@ -0,0 +1,5 @@
+zalign (0.9.1-1) UNRELEASED; urgency=low
+
+  * Initial release (Closes: #nnnn)
+
+ -- Steffen Moeller <moeller at debian.org>  Mon, 27 Aug 2012 15:14:15 +0200

Added: trunk/packages/zalign/trunk/debian/compat
===================================================================
--- trunk/packages/zalign/trunk/debian/compat	                        (rev 0)
+++ trunk/packages/zalign/trunk/debian/compat	2012-08-27 13:40:37 UTC (rev 12136)
@@ -0,0 +1 @@
+8

Added: trunk/packages/zalign/trunk/debian/control
===================================================================
--- trunk/packages/zalign/trunk/debian/control	                        (rev 0)
+++ trunk/packages/zalign/trunk/debian/control	2012-08-27 13:40:37 UTC (rev 12136)
@@ -0,0 +1,25 @@
+Source: zalign
+Section: science
+Priority: optional
+Maintainer: Steffen Moeller <moeller at debian.org>
+Build-Depends: debhelper (>= 8.0.0), autotools-dev, libopenmpi-dev
+Standards-Version: 3.9.3
+Homepage: https://launchpad.net/zalign
+#Vcs-Svn: git://git.debian.org/collab-maint/zalign.git
+#Vcs-Browser: http://git.debian.org/?p=collab-maint/zalign.git;a=summary
+
+Package: zalign
+Architecture: any
+Depends: ${shlibs:Depends}, ${misc:Depends}
+Description: parallel local alignment of biological sequences
+ zAlign is a local sequence aligner, especially intended for use with
+ large biological DNA sequences, with more than 1Mbp (Millions of base
+ pairs). It uses the Smith-Waterman exact algorithm with affine gap cost
+ function to perform this task.
+ .
+ zAlign can be used both in distributed (clusters, for
+ example) or standalone environments. Currently it has
+ been tested on Linux and Sun Solaris, using both the MPICH
+ (http://www.mcs.anl.gov/research/projects/mpi/mpich1/) and OpenMPI
+ (http://www.open-mpi.org/) implementations. Ports for other Unix-like
+ environments are highly considered.

Added: trunk/packages/zalign/trunk/debian/copyright
===================================================================
--- trunk/packages/zalign/trunk/debian/copyright	                        (rev 0)
+++ trunk/packages/zalign/trunk/debian/copyright	2012-08-27 13:40:37 UTC (rev 12136)
@@ -0,0 +1,34 @@
+Format: http://dep.debian.net/deps/dep5
+Upstream-Name: zalign
+Source: <url://example.com>
+
+Files: *
+Copyright: <years> <put author's name and email here>
+           <years> <likewise for another author>
+License: GPL-3.0+
+
+Files: debian/*
+Copyright: 2012 Steffen Moeller <moeller at debian.org>
+License: GPL-3.0+
+
+License: GPL-3.0+
+ This program is free software: you can redistribute it and/or modify
+ it under the terms of the GNU General Public License as published by
+ the Free Software Foundation, either version 3 of the License, or
+ (at your option) any later version.
+ .
+ This package is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ GNU General Public License for more details.
+ .
+ You should have received a copy of the GNU General Public License
+ along with this program. If not, see <http://www.gnu.org/licenses/>.
+ .
+ On Debian systems, the complete text of the GNU General
+ Public License version 3 can be found in "/usr/share/common-licenses/GPL-3".
+
+# Please also look if there are files or directories which have a
+# different copyright/license attached and list them here.
+# Please avoid to pick license terms that are more restrictive than the
+# packaged work, as it may make Debian's contributions unacceptable upstream.

Added: trunk/packages/zalign/trunk/debian/docs
===================================================================
--- trunk/packages/zalign/trunk/debian/docs	                        (rev 0)
+++ trunk/packages/zalign/trunk/debian/docs	2012-08-27 13:40:37 UTC (rev 12136)
@@ -0,0 +1,2 @@
+NEWS
+README

Added: trunk/packages/zalign/trunk/debian/rules
===================================================================
--- trunk/packages/zalign/trunk/debian/rules	                        (rev 0)
+++ trunk/packages/zalign/trunk/debian/rules	2012-08-27 13:40:37 UTC (rev 12136)
@@ -0,0 +1,15 @@
+#!/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
+
+export CXXFLAGS=-I/usr/lib/openmpi/include
+
+%:
+	dh $@  --with autotools-dev


Property changes on: trunk/packages/zalign/trunk/debian/rules
___________________________________________________________________
Added: svn:executable
   + *

Added: trunk/packages/zalign/trunk/debian/source/format
===================================================================
--- trunk/packages/zalign/trunk/debian/source/format	                        (rev 0)
+++ trunk/packages/zalign/trunk/debian/source/format	2012-08-27 13:40:37 UTC (rev 12136)
@@ -0,0 +1 @@
+3.0 (quilt)

Added: trunk/packages/zalign/trunk/debian/watch
===================================================================
--- trunk/packages/zalign/trunk/debian/watch	                        (rev 0)
+++ trunk/packages/zalign/trunk/debian/watch	2012-08-27 13:40:37 UTC (rev 12136)
@@ -0,0 +1,2 @@
+version=3
+https://launchpad.net/zalign/0.9/0.9.1/+download/zalign-([0-9.]+)\.tar\.gz


