altree (1.0.1-3) debian-dir only changes

--- altree-1.0.1.orig/debian/altree.doc-base
+++ altree-1.0.1/debian/altree.doc-base
@@ -0,0 +1,11 @@
+Document: altree
+Title: ALTree: Association and Localisation tests using haplotype phylogenetic Trees
+Author: Claire Bardel, Vincent Danjean, Pierre Darly and Emanuelle Guérin
+Abstract: This manual covers the installation and usage of ALTree. It provides a
+ reference for for the `ALTree-convert', `ALTree-add-S' and `ALTree' programs,
+ as well as explanation about the example files distributed in the
+ `altree-examples' Debian package.
+Section: Science/Biology
+
+Format: PDF
+Files: /usr/share/doc/altree/manual.pdf
--- altree-1.0.1.orig/debian/copyright
+++ altree-1.0.1/debian/copyright
@@ -0,0 +1,32 @@
+Format-Specification: http://wiki.debian.org/Proposals/CopyrightFormat?action=recall&rev=139
+Upstream-Author: Claire Bardel
+Packaged-By: Vincent Danjean <Vincent.Danjean@ens-lyon.org>
+Packaged-Date: Mon, 25 Jul 2005 22:22:50 +0200
+Original-Source-Location: http://claire.bardel.free.fr/files/altree-1.0.1.tar.gz
+
+Files: *
+Copyright: © 2005-2008 Claire Bardel <Claire.Bardel@univ-lyon1.fr>
+           © 2005-2007 Vincent Danjean <vdanjean.ml@free.fr>
+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.
+ .
+ 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 package; if not, write to the Free Software
+ Foundation, Inc., 51 Franklin St, Fifth Floor, Boston,
+ MA 02110-1301, USA.
+X-Comment: On Debian systems, the complete text of the GNU General
+ Public License can be found in `/usr/share/common-licenses/GPL'.
+
+Files: debian/*
+Copyright: © 2005—2008 Vincean Danjean <Vincent.Danjean@ens-lyon.org>
+           © 2008 David Paleino <d.paleino@gmail.com>
+           © 2008 Charles Plessy <plessy@debian.org>
+License: Same as altree
--- altree-1.0.1.orig/debian/watch
+++ altree-1.0.1/debian/watch
@@ -0,0 +1,2 @@
+version=3
+http://claire.bardel.free.fr/files/altree-([[:digit:]].*)\.tar\.gz
--- altree-1.0.1.orig/debian/rules
+++ altree-1.0.1/debian/rules
@@ -0,0 +1,14 @@
+#!/usr/bin/make -f
+
+DEB_COMPRESS_EXCLUDE := .pdf    # The PDF doc will not be compressed
+
+include /usr/share/cdbs/1/rules/debhelper.mk
+include /usr/share/cdbs/1/class/makefile.mk
+include /usr/share/cdbs/1/rules/patchsys-quilt.mk
+include /usr/share/cdbs/1/class/perlmodule.mk
+
+build/altree::
+	$(MAKE) -C Documentation pdf
+
+clean::
+	$(MAKE) -C Documentation distclean
--- altree-1.0.1.orig/debian/control
+++ altree-1.0.1/debian/control
@@ -0,0 +1,33 @@
+Source: altree
+Section: science
+Priority: optional
+Maintainer: Debian-Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
+DM-Upload-Allowed: yes
+Uploaders: Charles Plessy <plessy@debian.org>,
+ Vincent Danjean <vdanjean@debian.org>,
+ David Paleino <d.paleino@gmail.com>
+Build-Depends: debhelper (>= 5.0.0), quilt, patchutils (>= 0.2.25), cdbs (>= 0.4.27), perl (>= 5.6.0), latex-make, texlive-lang-french, texlive-latex-extra, texlive-latex-recommended, texlive-fonts-recommended
+Standards-Version: 3.8.0
+Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/altree/trunk/?rev=0&sc=0
+Vcs-Svn: svn://svn.debian.org/svn/debian-med/trunk/packages/altree
+Homepage: http://claire.bardel.free.fr/
+
+Package: altree
+Architecture: any
+Conflicts: libcutils-perl, alphy
+Replaces: libcutils-perl, alphy
+Provides: libcutils-perl, alphy
+Depends: ${shlibs:Depends}, ${misc:Depends}, ${perl:Depends}
+Suggests: altree-examples
+Description: program to perform phylogeny based analyses
+ ALTree was designed to perform phylogeny based analysis: first,
+ it allows the detection of an association between a candidate gene and
+ a disease, and second, it enables to make hypothesis about the
+ susceptibility loci.
+
+Package: altree-examples
+Architecture: all
+Recommends: altree (= ${binary:Version})
+Description: example files for ALTree
+ This package contains the example files for the ALTree package discussed in
+ its PDF manual.
--- altree-1.0.1.orig/debian/altree-examples.docs
+++ altree-1.0.1/debian/altree-examples.docs
@@ -0,0 +1 @@
+test/*
--- altree-1.0.1.orig/debian/compat
+++ altree-1.0.1/debian/compat
@@ -0,0 +1 @@
+5
--- altree-1.0.1.orig/debian/altree.docs
+++ altree-1.0.1/debian/altree.docs
@@ -0,0 +1,2 @@
+README
+Documentation/manual.pdf
--- altree-1.0.1.orig/debian/changelog
+++ altree-1.0.1/debian/changelog
@@ -0,0 +1,81 @@
+altree (1.0.1-3) unstable; urgency=low
+
+  * debian/control:
+    - Corrected the VCS information.
+    - Checked conformance with Policy 3.8.0 (no changes needed).
+    - Added a new Arch:all package, altree-examples.
+  * debian/copyright:
+    - Lifted to the latest version of the proposed machine-readable format.
+  * manual.pdf:
+    - Compression prevented by DEB_COMPRESS_EXCLUDE := .pdf in debian/rules.
+    - Registered in doc-base.
+
+ -- Charles Plessy <plessy@debian.org>  Sun, 22 Jun 2008 01:37:07 +0900
+
+altree (1.0.1-2) unstable; urgency=low
+
+  [ Charles Plessy ]
+  * Initial release for Debian (Closes: #461506)
+  * debian/copyright: converted to machine-readable format.
+  * debian/control:
+    - Added texlive-lang-french, texlive-latex-recommended
+      and texlive-latex-extra as build dependencies.
+    - Updated my email address.
+
+  [ David Paleino ]
+  * Added debian/watch
+  * debian/compat and debhelper dependency updated
+  * debian/control:
+    - added myself in Uploaders
+    - Standards-Version is now 3.7.3
+
+  [ Vincent Danjean ]
+  * remove unused debian/control.in file
+  * Fix copyright (and update email addresses)
+  * Fix build-depends:
+    + remove debian part of version (thanks lintian)
+    + change latex-utils to latex-make (always present with this name in
+      Debian)
+  * Fix depends: add ${perl:Depends}
+  * remove empty dir in package (/usr/sbin)
+  => package lintian clean now
+
+ -- Charles Plessy <plessy@debian.org>  Mon, 12 May 2008 13:37:03 +0900
+
+altree (1.0.1-1) unstable; urgency=low
+
+  * New upstream release
+
+ -- Vincent Danjean <Vincent.Danjean@ens-lyon.org>  Fri, 13 Jan 2006 15:46:52 +0100
+
+altree (1.0.0-1) unstable; urgency=low
+
+  * New upstream release
+
+ -- Vincent Danjean <Vincent.Danjean@ens-lyon.org>  Fri, 13 Jan 2006 09:40:02 +0100
+
+altree (0.9.2-2) unstable; urgency=low
+
+  * Update FSF address in copyright file
+
+ -- Vincent Danjean <Vincent.Danjean@ens-lyon.org>  Sat, 10 Sep 2005 10:25:23 +0200
+
+altree (0.9.2-1) unstable; urgency=low
+
+  * New upstream release
+  * New upstream name
+
+ -- Vincent Danjean <Vincent.Danjean@ens-lyon.org>  Tue,  2 Aug 2005 19:52:19 +0200
+
+alphy (0.9.1d-1) unstable; urgency=low
+
+  * New upstream release
+
+ -- Vincent Danjean <Vincent.Danjean@ens-lyon.org>  Tue, 26 Jul 2005 00:08:40 +0200
+
+alphy (0.9.1c-1) unstable; urgency=low
+
+  * Initial release
+
+ -- Vincent Danjean <Vincent.Danjean@ens-lyon.org>  Mon, 25 Jul 2005 22:22:50 +0200
+