--- exonerate-2.2.0.orig/debian/watch
+++ exonerate-2.2.0/debian/watch
@@ -0,0 +1,3 @@
+version=3
+http://www.ebi.ac.uk/~guy/exonerate/exonerate-([0-9.]*)\.tar\.gz
+
--- exonerate-2.2.0.orig/debian/copyright
+++ exonerate-2.2.0/debian/copyright
@@ -0,0 +1,39 @@
+Format-Specification: http://wiki.debian.org/Proposals/CopyrightFormat?action=recall&rev=129
+Upstream-Author: Guy St.C. Slater <guy AT ebi.ac.uk>
+                                  <guy.slater AT gmail.com>
+ The following have contributed code to this project:
+ (in chronological order)
+    Ewan Birney      <birney-AT-ebi.ac.uk>
+    Ian Holmes       <ihh-AT-fruitfly.org>
+    Steve Searle     <searle-AT-sanger.ac.uk>
+    Tim Cutts        <tjrc-AT-sanger.ac.uk>
+    Don Gilbert      <gilbertd-AT-indiana.edu>
+    Michael Schuster <michaels-AT-ebi.ac.uk>
+Packaged-By: This package was debianized by Steffen Moeller <moeller@debian.org>
+Packaged-Date: Mon, 02 Jul 2007 11:42:38 +0200
+Original-Source-Location: http://www.ebi.ac.uk/~guy/exonerate/exonerate-2.0.0.tar.gz
+
+Files: *
+Copyright: © 2000-2008 Guy St.C. Slater <guy AT ebi.ac.uk>
+                                        <guy.slater AT gmail.com>
+License: GPL-3+
+ 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 program 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/>.
+X-Comment: On Debian GNU/Linux systems, the complete text of the GNU General
+ Public License can be found in `/usr/share/common-licenses/GPL'
+
+Files: debian/*
+Copyright: © 2007 Steffen Moeller <moeller@debian.org>
+           © 2008 Charles Plessy <plessy@debian.org>
+License: GPL-3+
+ (see above)
--- exonerate-2.2.0.orig/debian/changelog
+++ exonerate-2.2.0/debian/changelog
@@ -0,0 +1,79 @@
+exonerate (2.2.0-2) unstable; urgency=low
+
+  [ Charles Plessy ]
+  * debian/control:
+    - Enhances bioperl-run instead of bioperl.
+    - Incremented Standards-Version to reflect conformance with Policy
+      3.8.3 (no changes needed).
+
+  [ Andreas Tille ]
+  * debian/control
+    - s/libreadline5-dev/libreadline-dev/
+    - s/Debian-Med/Debian Med/
+
+ -- Andreas Tille <tille@debian.org>  Sun, 13 Sep 2009 17:34:07 +0200
+
+exonerate (2.2.0-1) unstable; urgency=low
+
+  * New upstream release (LP: #285237).
+    This version includes fixes for problems with excessive memory consumption
+    when compiled against glib-2, and fixes a bug with using exonerate-server
+    with unmasked sequences. 
+
+ -- Charles Plessy <plessy@debian.org>  Mon, 20 Oct 2008 14:18:36 +0200
+
+exonerate (2.1.0-1) unstable; urgency=low
+
+  * New upstream release (LP: #254115).
+    - This version includes many optimisations and bug fixes for the
+      exonerate-server. It is now possible to search a whole human-sized
+      genome with a typical cDNA or protein query in under a second.
+    - Exonerate-server uses use pthreads by default.
+  * debian/control, debian/compat: switched to debhelper 7.
+  * debian/control:
+    - Checked conformance with Policy 3.8.0.
+    - Enhances: bioperl.
+  * debian/rules:
+    - `--enable-glib2' removed as now default.
+    - Activated tests after build.
+  * Updated debian/copyright.
+
+ -- Charles Plessy <plessy@debian.org>  Mon, 04 Aug 2008 19:13:05 +0900
+
+exonerate (2.0.0-1) unstable; urgency=low
+
+  [ David Paleino ]
+  * Updated to Standards-Version 3.8.0 (no changes needed)
+
+  [ Charles Plessy ]
+  * New upstream release (Closes: #479323)
+    Quoting the upstream changelog:
+    o Modified exonerate to work in Client:Server mode
+    o Fixed --refine to work with SDP alignments
+    o Disabled codegen warnings from bootstrapper during compilation
+    o Added --geneticcode option for using alternative genetic codes
+    o Added --splice5 and --splice3 to allow alternative splice site PSSMs
+    o Fixed several bugs when scanning query sequences (eg. --forcescan query)
+    o Fixed to report query on forward strand whenever possible.
+    o Fixed --ryo sequence dumping with --bestn
+    o Fixed a bug with missing seeds when using --annotation
+    o Changed license to GPLv3
+    o Added protein2dna:bestfit and protein2genome:bestfit models
+      (works with exhaustive alignment only)
+  * Updated my email address.
+  * debian/control:
+    - Building on glib-2.0 instead of 1.2.
+    - Added a build dependency on libreadline5-dev.
+    - Augmented the long description and changed the short.
+    - Added a build dependency on CDBS.
+  * debian/copyright made machine-readable.
+  * debian/rules switched to cdbs.
+  * debian/dirs: removed.
+
+ -- Charles Plessy <plessy@debian.org>  Wed, 02 Jul 2008 11:24:48 +0900
+
+exonerate (1.4.0-1) unstable; urgency=low
+
+  * Initial release (Closes: #431404).
+
+ -- Steffen Moeller <moeller@debian.org>  Mon, 02 Jul 2007 11:42:38 +0200
--- exonerate-2.2.0.orig/debian/README.Debian
+++ exonerate-2.2.0/debian/README.Debian
@@ -0,0 +1,16 @@
+exonerate for Debian
+--------------------
+
+Charles has fixed the man pages for this package - many thanks to him.
+
+The upstream author, Guy Slater, is very supportive of Debian. He even
+gave brief instructions on how to build a package in his README. 
+This is much appreciated.
+
+Guy was contacted asking for a clarification of the version of the
+GPL he refers to and to avoid the web link in the C sources to a (now)
+later version than he distributes with the source.
+
+Steffen
+
+ -- Steffen Moeller <moeller@debian.org>  Mon, 02 Jul 2007 11:42:38 +0200
--- exonerate-2.2.0.orig/debian/links
+++ exonerate-2.2.0/debian/links
@@ -0,0 +1,25 @@
+usr/share/man/man1/fastaoverlap.1.gz 	usr/share/man/man1/exonerate-client.1.gz
+usr/share/man/man1/fastaoverlap.1.gz	usr/share/man/man1/exonerate-server.1.gz
+usr/share/man/man1/fastaoverlap.1.gz	usr/share/man/man1/fasta2esd.1.gz
+usr/share/man/man1/fastaoverlap.1.gz	usr/share/man/man1/fastaannotatecdna.1.gz
+usr/share/man/man1/fastaoverlap.1.gz	usr/share/man/man1/fastachecksum.1.gz
+usr/share/man/man1/fastaoverlap.1.gz	usr/share/man/man1/fastaclean.1.gz
+usr/share/man/man1/fastaoverlap.1.gz	usr/share/man/man1/fastaclip.1.gz
+usr/share/man/man1/fastaoverlap.1.gz	usr/share/man/man1/fastacomposition.1.gz
+usr/share/man/man1/fastaoverlap.1.gz	usr/share/man/man1/fastadiff.1.gz
+usr/share/man/man1/fastaoverlap.1.gz	usr/share/man/man1/fastaexplode.1.gz
+usr/share/man/man1/fastaoverlap.1.gz	usr/share/man/man1/fastafetch.1.gz
+usr/share/man/man1/fastaoverlap.1.gz	usr/share/man/man1/fastahardmask.1.gz 
+usr/share/man/man1/fastaoverlap.1.gz	usr/share/man/man1/fastaindex.1.gz
+usr/share/man/man1/fastaoverlap.1.gz	usr/share/man/man1/fastalength.1.gz
+usr/share/man/man1/fastaoverlap.1.gz	usr/share/man/man1/fastanrdb.1.gz
+usr/share/man/man1/fastaoverlap.1.gz	usr/share/man/man1/fastareformat.1.gz
+usr/share/man/man1/fastaoverlap.1.gz	usr/share/man/man1/fastaremove.1.gz
+usr/share/man/man1/fastaoverlap.1.gz	usr/share/man/man1/fastarevcomp.1.gz
+usr/share/man/man1/fastaoverlap.1.gz	usr/share/man/man1/fastasoftmask.1.gz
+usr/share/man/man1/fastaoverlap.1.gz	usr/share/man/man1/fastasort.1.gz
+usr/share/man/man1/fastaoverlap.1.gz	usr/share/man/man1/fastasplit.1.gz
+usr/share/man/man1/fastaoverlap.1.gz	usr/share/man/man1/fastasubseq.1.gz
+usr/share/man/man1/fastaoverlap.1.gz	usr/share/man/man1/fastatranslate.1.gz
+usr/share/man/man1/fastaoverlap.1.gz	usr/share/man/man1/fastavalidcds.1.gz
+	
--- exonerate-2.2.0.orig/debian/compat
+++ exonerate-2.2.0/debian/compat
@@ -0,0 +1 @@
+7
--- exonerate-2.2.0.orig/debian/rules
+++ exonerate-2.2.0/debian/rules
@@ -0,0 +1,6 @@
+#!/usr/bin/make -f
+
+include /usr/share/cdbs/1/class/autotools.mk
+include /usr/share/cdbs/1/rules/debhelper.mk
+
+DEB_MAKE_CHECK_TARGET = -C test check
--- exonerate-2.2.0.orig/debian/reference
+++ exonerate-2.2.0/debian/reference
@@ -0,0 +1,13 @@
+@Article{15713233,
+AUTHOR = { Slater, Guy and Birney, Ewan},
+TITLE = {Automated generation of heuristics for biological sequence comparison},
+JOURNAL = {BMC Bioinformatics},
+VOLUME = {6},
+YEAR = {2005},
+NUMBER = {1},
+PAGES = {31},
+URL = {http://www.biomedcentral.com/1471-2105/6/31},
+DOI = {10.1186/1471-2105-6-31},
+PubMedID = {15713233},
+ISSN = {1471-2105},
+}
--- exonerate-2.2.0.orig/debian/exonerate.manpages
+++ exonerate-2.2.0/debian/exonerate.manpages
@@ -0,0 +1,2 @@
+doc/man/man1/*.1
+debian/manpages/fastaoverlap.1
--- exonerate-2.2.0.orig/debian/control
+++ exonerate-2.2.0/debian/control
@@ -0,0 +1,33 @@
+Source: exonerate
+Section: science
+Priority: optional
+Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
+DM-Upload-Allowed: yes
+Uploaders: Steffen Moeller <moeller@debian.org>,
+ Charles Plessy <plessy@debian.org>,
+ Andreas Tille <tille@debian.org>
+Build-Depends: debhelper (>= 7.1), autotools-dev, libglib2.0-dev, libreadline-dev, cdbs
+Standards-Version: 3.8.3
+Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/exonerate/trunk/?rev=0&sc=0
+Vcs-Svn: svn://svn.debian.org/svn/debian-med/trunk/packages/exonerate/trunk/
+Homepage: http://www.ebi.ac.uk/~guy/exonerate/
+
+Package: exonerate
+Architecture: any
+Depends: ${shlibs:Depends}, ${misc:Depends}
+Suggests: wise
+Enhances: bioperl-run
+Description: generic tool for pairwise sequence comparison
+ Exonerate allows you to align sequences using a many alignment models, using
+ either exhaustive dynamic programming, or a variety of heuristics. Much of
+ the functionality of the Wise dynamic programming suite was reimplemented in C
+ for better efficiency. Exonerate is an intrinsic component of the building of
+ the Ensembl genome databases, providing similarity scores between RNA and DNA
+ sequences and thus determining splice variants and coding sequences in
+ general.
+ .
+ An In-silico PCR Experiment Simulation System (see the ipcress man page) is
+ packaged with exonerate.
+ .
+ This package also comes with a selection of utilities for performing
+ simple manipulations quickly on fasta files beyond 2Gb
--- exonerate-2.2.0.orig/debian/docs
+++ exonerate-2.2.0/debian/docs
@@ -0,0 +1,4 @@
+README
+TODO
+AUTHORS
+ChangeLog
--- exonerate-2.2.0.orig/debian/manpages/fastaoverlap.1
+++ exonerate-2.2.0/debian/manpages/fastaoverlap.1
@@ -0,0 +1,122 @@
+.\"                                      Hey, EMACS: -*- nroff -*-
+.\" First parameter, NAME, should be all caps
+.\" Second parameter, SECTION, should be 1-8, maybe w/ subsection
+.\" other parameters are allowed: see man(7), man(1)
+.TH EXONERATE 1 "30 Jun 2007"
+.\" Please adjust this date whenever revising the manpage.
+.\"
+.\" Some roff macros, for reference:
+.\" .nh        disable hyphenation
+.\" .hy        enable hyphenation
+.\" .ad l      left justify
+.\" .ad b      justify to both left and right margins
+.\" .nf        disable filling
+.\" .fi        enable filling
+.\" .br        insert line break
+.\" .sp <n>    insert n+1 empty lines
+.\" for manpage-specific macros, see man(7)
+.SH NAME
+exonerate \- suite for investigating DNA and RNA sequence similarities
+.SH SYNOPSIS
+.B exonerate-client
+.RI [ --help ]
+.br
+.B exonerate-server
+.RI [ --help ]
+.br
+.B fasta2esd
+.RI [ --help ]
+.br
+.B fastaannotatecdna
+.RI [ --help ]
+.br
+.B fastachecksum
+.RI [ --help ]
+.br
+.B fastaclean
+.RI [ --help ]
+.br
+.B fastaclip
+.RI [ --help ]
+.br
+.B fastacomposition
+.RI [ --help ]
+.br
+.B fastadiff
+.RI [ --help ]
+.br
+.B fastaexplode
+.RI [ --help ]
+.br
+.B fastafetch
+.RI [ --help ]
+.br
+.B fastahardmask
+.RI [ --help ]
+.br
+.B fastaindex
+.RI [ --help ]
+.br
+.B fastalength
+.RI [ --help ]
+.br
+.B fastanrdb
+.RI [ --help ]
+.br
+.B fastaoverlap
+.RI [ --help ]
+.br
+.B fastareformat
+.RI [ --help ]
+.br
+.B fastaremove
+.RI [ --help ]
+.br
+.B fastarevcomp
+.RI [ --help ]
+.br
+.B fastasoftmask
+.RI [ --help ]
+.br
+.B fastasort
+.RI [ --help ]
+.br
+.B fastasplit
+.RI [ --help ]
+.br
+.B fastasubseq
+.RI [ --help ]
+.br
+.B fastatranslate
+.RI [ --help ]
+.br
+.B fastavalidcds
+.RI [ --help ]
+.br
+.SH DESCRIPTION
+These programs are not described by the upstream author, however, some information
+is available via the --help and -h arguments for all these programs. Whoever is using
+any of these programs in routine, is requested to provide a seed of a respective man page
+to the upstream author.
+.PP
+.SH OPTIONS
+.TP
+.B \-h,
+.B \-\-help
+Show summary of options.
+.TP
+.B \-v, \-\-version
+Show version of program.
+.SH SEE ALSO
+.BR http://www.ebi.ac.uk/~guy/exonerate/
+.br
+The author of this package provides a beginner (
+.IR http://www.ebi.ac.uk/~guy/exonerate/beginner.html
+) and and avanced 
+.RI http://www.ebi.ac.uk/~guy/exonerate/advanced.html
+) tutorial on his web pages.
+.SH AUTHOR
+exonerate was written by Guy Slater <guy@ebi.ac.uk>.
+.PP
+This manual page was written by Steffen Moeller
+for the Debian project (but may be used by others).