[med-svn] r1579 - in trunk/packages: . mauvealign mauvealign/trunk mauvealign/trunk/debian mauvealign/trunk/debian/patches
tille at alioth.debian.org
tille at alioth.debian.org
Thu Mar 13 21:44:21 UTC 2008
Author: tille
Date: 2008-03-13 21:44:20 +0000 (Thu, 13 Mar 2008)
New Revision: 1579
Added:
trunk/packages/mauvealign/
trunk/packages/mauvealign/trunk/
trunk/packages/mauvealign/trunk/debian/
trunk/packages/mauvealign/trunk/debian/README.Debian
trunk/packages/mauvealign/trunk/debian/changelog
trunk/packages/mauvealign/trunk/debian/compat
trunk/packages/mauvealign/trunk/debian/control
trunk/packages/mauvealign/trunk/debian/copyright
trunk/packages/mauvealign/trunk/debian/patches/
trunk/packages/mauvealign/trunk/debian/patches/10_dynamic.patch
trunk/packages/mauvealign/trunk/debian/patches/series
trunk/packages/mauvealign/trunk/debian/rules
trunk/packages/mauvealign/trunk/debian/watch
Log:
Initial inject of mauvealign, needs libMems and libClustalW that are not (yet)
in Debian but at people.debian.org/~tille/packages
Added: trunk/packages/mauvealign/trunk/debian/README.Debian
===================================================================
--- trunk/packages/mauvealign/trunk/debian/README.Debian (rev 0)
+++ trunk/packages/mauvealign/trunk/debian/README.Debian 2008-03-13 21:44:20 UTC (rev 1579)
@@ -0,0 +1,12 @@
+MauveAligner for Debian
+-----------------------
+
+ATTENTION:
+This package build-depends from libclustalw which has some
+license issues and thus can not be distributed by Debian
+for the moment. There are unofficial packages avialable
+from
+
+ http://people.debian.org/~tille/packages/libclustalw/
+
+ -- Andreas Tille <tille at debian.org> Thu, 14 Feb 2008 22:13:45 +0100
Added: trunk/packages/mauvealign/trunk/debian/changelog
===================================================================
--- trunk/packages/mauvealign/trunk/debian/changelog (rev 0)
+++ trunk/packages/mauvealign/trunk/debian/changelog 2008-03-13 21:44:20 UTC (rev 1579)
@@ -0,0 +1,5 @@
+mauvealigner (1.0.0-1) unstable; urgency=low
+
+ * Initial release (Closes: #??????)
+
+ -- Andreas Tille <tille at debian.org> Thu, 13 Mar 2008 15:16:59 +0100
Added: trunk/packages/mauvealign/trunk/debian/compat
===================================================================
--- trunk/packages/mauvealign/trunk/debian/compat (rev 0)
+++ trunk/packages/mauvealign/trunk/debian/compat 2008-03-13 21:44:20 UTC (rev 1579)
@@ -0,0 +1 @@
+6
Added: trunk/packages/mauvealign/trunk/debian/control
===================================================================
--- trunk/packages/mauvealign/trunk/debian/control (rev 0)
+++ trunk/packages/mauvealign/trunk/debian/control 2008-03-13 21:44:20 UTC (rev 1579)
@@ -0,0 +1,43 @@
+Source: mauvealigner
+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 (>= 6), cdbs, quilt, libmems-1.5-1-dev, libboost-graph-dev
+Standards-Version: 3.7.3
+Section: science
+Homepage: http://asap.ahabs.wisc.edu/mauve/
+Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/mauvealigner/?rev=0&sc=0
+Vcs-Svn: svn://svn.debian.org/svn/debian-med/trunk/packages/mauvealigner/trunk/
+
+Package: mauvealigner
+Section: science
+Architecture: any
+Enhances: mauve
+Depends: ${devlibs:Depends}
+Description: multiple genome alignment algorithms
+ The mauveAligner and progressiveMauve alignment algorithms have been
+ implemented as command-line programs included with the downloadable Mauve
+ software. When run from the command-line, these programs provide options
+ not yet available in the graphical interface.
+ .
+ Mauve is a system for efficiently constructing multiple genome alignments
+ in the presence of large-scale evolutionary events such as rearrangement
+ and inversion. Multiple genome alignment provides a basis for research
+ into comparative genomics and the study of evolutionary dynamics. Aligning
+ whole genomes is a fundamentally different problem than aligning short
+ sequences.
+ .
+ Mauve has been developed with the idea that a multiple genome aligner
+ should require only modest computational resources. It employs algorithmic
+ techniques that scale well in the amount of sequence being aligned. For
+ example, a pair of Y. pestis genomes can be aligned in under a minute,
+ while a group of 9 divergent Enterobacterial genomes can be aligned in
+ a few hours.
+ .
+ Mauve computes and interactively visualizes genome sequence comparisons.
+ Using FastA or GenBank sequence data, Mauve constructs multiple genome
+ alignments that identify large-scale rearrangement, gene gain, gene loss,
+ indels, and nucleotide substutition.
+ .
+ Mauve is developed at the University of Wisconsin.
Added: trunk/packages/mauvealign/trunk/debian/copyright
===================================================================
--- trunk/packages/mauvealign/trunk/debian/copyright (rev 0)
+++ trunk/packages/mauvealign/trunk/debian/copyright 2008-03-13 21:44:20 UTC (rev 1579)
@@ -0,0 +1,24 @@
+X-Format-Specification: http://wiki.debian.org/Proposals/CopyrightFormat
+X-Debianized-By: Andreas Tille <tille at debian.org>
+X-Debinized-Date: Thu, 13 Mar 2008 15:16:59 +0100
+X-Source-Downloaded-From: http://gel.ahabs.wisc.edu/mauve/source/mauve_2.1.1/
+X-Upstream-Author: © 2003, 2004, 2005, 2006, 2007, Aaron Darling -- darling at cs.wisc.edu
+
+Files: debian/*
+Copyright: © 2008, Andreas Tille <tille at debian.org>
+License: GPL-2+
+ This package 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 2 of the License, or
+ (at your option) any later version.
+
+Files: *
+Copyright: © 2003, 2004, 2005, 2006, 2007, Aaron Darling -- darling at cs.wisc.edu
+
+License: GPL-2
+ This package 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 version 2 of the License.
+
+On Debian systems, the complete text of the licenses can be found in:
+GPL-2 - `/usr/share/common-licenses/GPL-2'
Added: trunk/packages/mauvealign/trunk/debian/patches/10_dynamic.patch
===================================================================
--- trunk/packages/mauvealign/trunk/debian/patches/10_dynamic.patch (rev 0)
+++ trunk/packages/mauvealign/trunk/debian/patches/10_dynamic.patch 2008-03-13 21:44:20 UTC (rev 1579)
@@ -0,0 +1,11 @@
+--- mauvealigner-1.0.0.orig/configure
++++ mauvealigner-1.0.0/configure
+@@ -4339,7 +4339,7 @@
+
+
+
+-STATIC_FLAG="-static"
++STATIC_FLAG=""
+ if ( test "x$target_vendor" = "xapple") then
+ STATIC_FLAG=""
+ fi
Added: trunk/packages/mauvealign/trunk/debian/patches/series
===================================================================
--- trunk/packages/mauvealign/trunk/debian/patches/series (rev 0)
+++ trunk/packages/mauvealign/trunk/debian/patches/series 2008-03-13 21:44:20 UTC (rev 1579)
@@ -0,0 +1 @@
+10_dynamic.patch
Added: trunk/packages/mauvealign/trunk/debian/rules
===================================================================
--- trunk/packages/mauvealign/trunk/debian/rules (rev 0)
+++ trunk/packages/mauvealign/trunk/debian/rules 2008-03-13 21:44:20 UTC (rev 1579)
@@ -0,0 +1,8 @@
+#!/usr/bin/make -f
+
+include /usr/share/cdbs/1/rules/patchsys-quilt.mk
+include /usr/share/cdbs/1/rules/debhelper.mk
+include /usr/share/cdbs/1/class/autotools.mk
+
+# Do not force -static linking
+DEB_CONFIGURE_SCRIPT_ENV += STATIC_FLAG=""
Property changes on: trunk/packages/mauvealign/trunk/debian/rules
___________________________________________________________________
Name: svn:executable
+ *
Added: trunk/packages/mauvealign/trunk/debian/watch
===================================================================
--- trunk/packages/mauvealign/trunk/debian/watch (rev 0)
+++ trunk/packages/mauvealign/trunk/debian/watch 2008-03-13 21:44:20 UTC (rev 1579)
@@ -0,0 +1,3 @@
+version=3
+
+http://gel.ahabs.wisc.edu/mauve/source/mauve_(.*)/mauvealigner-(.*)\.tar\.gz
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