--- gff2ps-0.98d.orig/gff2ps_v0.98d
+++ gff2ps-0.98d/gff2ps_v0.98d
@@ -39,7 +39,7 @@
 # Only for testing (only works in bash)
 # set -o xtrace
 
-GAWK="/usr/bin/gawk";
+GAWK="/usr/local/bin/gawk";
 
 ##############################################################
 #################### PROGRAM DEFINITIONS #####################
--- gff2ps-0.98d.orig/debian/linda.override
+++ gff2ps-0.98d/debian/linda.override
@@ -0,0 +1,2 @@
+Tag: exec-not-elf-or-script
+Data: /usr/share/gff2ps/gff2ps.real
--- gff2ps-0.98d.orig/debian/control
+++ gff2ps-0.98d/debian/control
@@ -0,0 +1,25 @@
+Source: gff2ps
+Section: science
+Priority: optional
+Maintainer: Debian-Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
+DM-Upload-Allowed: yes
+Uploaders: Nelson A. de Oliveira <naoliv@debian.org>
+Build-Depends: cdbs, debhelper (>= 5)
+Standards-Version: 3.7.3
+Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/gff2ps/trunk/
+Vcs-Svn: svn://svn.debian.org/svn/debian-med/trunk/packages/gff2ps/trunk/
+Homepage: http://genome.imim.es/software/gfftools/GFF2PS.html
+
+Package: gff2ps
+Architecture: all
+Depends: gawk, ${misc:Depends}
+Recommends: gv | postscript-viewer
+Description: produces PostScript graphical output from GFF-files
+ gff2ps is a script program developed with the aim of converting gff-formatted
+ records into high quality one-dimensional plots in PostScript. Such plots
+ maybe useful for comparing genomic structures and to visualizing outputs from
+ genome annotation programs.
+ It can be used in a very simple way, because it assumes that the GFF file
+ itself carries enough formatting information, but it also allows through a
+ number of options and/or a configuration file, for a great degree of
+ customization.
--- gff2ps-0.98d.orig/debian/manpages
+++ gff2ps-0.98d/debian/manpages
@@ -0,0 +1 @@
+debian/gff2ps.1
--- gff2ps-0.98d.orig/debian/patches/01-gff2ps_v0.98d.diff
+++ gff2ps-0.98d/debian/patches/01-gff2ps_v0.98d.diff
@@ -0,0 +1,11 @@
+--- gff2ps_v0.98d	2005-03-22 12:23:09.000000000 -0300
++++ gff2ps_v0.98d-new	2005-03-22 12:23:49.000000000 -0300
+@@ -39,7 +39,7 @@
+ # Only for testing (only works in bash)
+ # set -o xtrace
+ 
+-GAWK="/usr/local/bin/gawk";
++GAWK="/usr/bin/gawk";
+ 
+ ##############################################################
+ #################### PROGRAM DEFINITIONS #####################
--- gff2ps-0.98d.orig/debian/gff2ps.1
+++ gff2ps-0.98d/debian/gff2ps.1
@@ -0,0 +1,147 @@
+.TH GFF2PS 1 "Tue, 22 Mar 2005 12:58:35 -0300"
+.SH NAME
+gff2ps \- Produces PostScript graphical output from GFF-files.
+.SH SYNOPSIS
+.B gff2ps
+.RI "[options] -- gff_files"
+.SH DESCRIPTION
+This program draws color-filled DotPlots from files with gff-formatted data fields. The program takes as input the annotated features on a genomic sequence in GFF format, and produces a visual output in PostScript.
+.SH OPTIONS
+.TP
+.B \-h
+Show summary of options.
+.TP
+.B \-H <option>
+Shows only help for the especified option.
+.TP
+.B \-V
+Verbose mode, a full report is sent to standard error (default only sends Warnings).
+.TP
+.B \-v
+Silent mode: Disable all warnings, no messages sent to standard error.
+.TP
+.B \-d
+Write (or rewrite if exists) default customfile.
+.TP
+.B \-D <default_custom_filename>
+Create a new default customfile with the given filename.
+.TP
+.B \-C <custom_filename>
+Load given custom file and append to default custom file (.gff2psrc).
+.TP
+.B \-s <page_size>
+Useful to modify page size (default is a4).
+.TP
+.B \-p
+Switches page orientation to Portrait (default is Landscape).
+.TP
+.B \-G <color_name>
+Sets color for FOREGROUND (default is black).
+.TP
+.B \-g <color_name>
+Sets color for BACKGROUND (default is white).
+.TP
+.B \-P <#>
+Sets how many pages are needed to split your output (default is one).
+.TP
+.B \-S <#>
+Zoom first nucleotide (default is sequence origin).
+.TP
+.B \-E <#>
+Zoom last nucleotide (default is sequence length).
+.TP
+.B \-B <#>
+Sets blocks per page (default is one).
+.TP
+.B \-N <#>
+Sets nucleotides per line (default is the largest sequence position from input gff-files).
+.TP
+.B \-b
+Blocks from left to right and from top to bottom (default is top to bottom first).
+.TP
+.B \-L
+Switch off Header (Title area).
+.TP
+.B \-T <title_string>
+Defining title (default is input gff filename).
+.TP
+.B \-t <subtitle_string>
+Defining subtitle (default is none).
+.TP
+.B \-l
+Does not show page numbering.
+.TP
+.B \-O
+Does not show date.
+.TP
+.B \-o
+Does not show time.
+.TP
+.B \-M <#>
+Number of major tickmarks per line (default 10).
+.TP
+.B \-K <#>
+Major tickmarks scale in nucleotides, default is nucleotide length for lines divided by major tickmarks number (see option -T).
+.TP
+.B \-m <#>
+Number of minor tickmarks between major tickmarks (default 10).
+.TP
+.B \-k <#>
+Minor tickmarks scale in nucleotides default is major tickmarks size divided by minor tickmarks number (see option -t).
+.TP
+.B \-w, \-f
+Switch off displaying forward-strand(Watson) elements.
+.TP
+.B \-c, \-r
+Switch off displaying reverse-strand(Crick) elements.
+.TP
+.B \-i
+Switch off displaying strand-independent elements.
+.TP
+.B \-0 <color_name>
+Sets color for frame "0" (default is blue).
+.TP
+.B \-1
+Sets color for frame "1" (default is red).
+.TP
+.B \-2
+Sets color for frame "2" (default is green).
+.TP
+.B \-3
+Sets color for frame "." (default is orange).
+.TP
+.B \-n
+Switch off labels for element positions.
+.TP
+.B \-a
+Switch off CopyRight line on plot.
+.SH ENVIRONMENT VARIABLES
+There are three environmental variables that can be set by users to their pre
+ferences:
+
+ + You can specify the path where GFF2PS can find the default files with the shell variable "GFF2PS_CFDIR". Default value is path where you are running GFF2PS.
+ + You can also define the default custom filename you will like with the variable "GFF2PS_CUSTOMFILE", program default filename for custom file is ".gff2psrc".
+ + GFF2PS needs to write few temporary files in a directory with permissions for current user to read and write. Default temporary directory path is set to "/tmp/" but you can assign a different temporary directory path using the variable "GFF2PS_TMP".
+
+Setting those vars in Bourne-shell (bash):
+   export GFF2PS_CFDIR="path"
+   export GFF2PS_CUSTOMFILE="file_name"
+   export GFF2PS_TMP="path"
+
+Using a C-Shell (csh):
+   setenv GFF2PS_CFDIR "path"
+   setenv GFF2PS_CUSTOMFILE "file_name"
+   setenv GFF2PS_TMP "path"
+.SH COMMENTS
+* Colors defined are:
+   Basic Colors: black white
+   Variable Colors: grey magenta violet blue skyblue cyan seagreen green lime green yellow orange red brown
+   You can get five color shades from Variable Colors with "verydark", "dark", "light" and "verylight" prefixes. An example: verydarkseagreen darkseagreen seagreen lightseagreen verylightseagreen
+
+* Page Sizes defined are:
+   From A0 to A10, from B0 to B10, 10x14, executive, folio, ledger, legal, letter, quarto, statement and tabloid.
+.SH AUTHOR
+gff2ps was written by Josep Francesc ABRIL FERRANDO <jabril@imim.es>.
+.PP
+This manual page was written by Nelson A. de Oliveira <naoliv@gmail.com>,
+for the Debian project (but may be used by others).
--- gff2ps-0.98d.orig/debian/changelog
+++ gff2ps-0.98d/debian/changelog
@@ -0,0 +1,28 @@
+gff2ps (0.98d-3) unstable; urgency=low
+
+  * Updated Standards-Version;
+  * Changed Maintainer to the Debian-Med Packaging Team;
+  * Added new Homepage field;
+  * Added Vcs-* fields.
+
+ -- Nelson A. de Oliveira <naoliv@debian.org>  Sun, 24 Feb 2008 00:18:36 -0300
+
+gff2ps (0.98d-2) unstable; urgency=low
+
+  * Updated debian/copyright file;
+  * Bumped Standards-Version to 3.7.2 (no changes needed);
+  * Moved cdbs and debhelper to Build-Depends;
+  * Using debhelper compatibility level 5;
+  * New debian/linda.override:
+    - Updated debian/rules to install the override.
+  * Removed "ghostview" from Recommends;
+  * Added a space before Homepage: on the package long description.
+
+ -- Nelson A. de Oliveira <naoliv@gmail.com>  Thu, 27 Jul 2006 02:28:37 -0300
+
+gff2ps (0.98d-1) unstable; urgency=low
+
+  * Initial Release (Closes: #310518).
+
+ -- Nelson A. de Oliveira <naoliv@gmail.com>  Tue, 22 Mar 2005 12:22:50 -0300
+
--- gff2ps-0.98d.orig/debian/copyright
+++ gff2ps-0.98d/debian/copyright
@@ -0,0 +1,28 @@
+This package was debianized by Nelson A. de Oliveira <naoliv@gmail.com> on
+Tue, 22 Mar 2005 12:22:50 -0300.
+
+It was downloaded from http://genome.imim.es/software/gfftools/GFF2PS.html
+
+gff2ps
+
+     Converting GFF files to PostScript.
+
+   Copyright (C) 1999-2003 - Josep Francesc ABRIL FERRANDO  
+                                    Roderic GUIGO SERRA       
+
+ 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 2 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, write to the Free Software
+ Foundation, Inc., 51 Franklin St, Fifth Floor, Boston,
+ MA 02110-1301, USA.
+
+On Debian systems, the GPL license can be found at /usr/share/common-licenses/
--- gff2ps-0.98d.orig/debian/install
+++ gff2ps-0.98d/debian/install
@@ -0,0 +1 @@
+debian/wrapper/gff2ps usr/bin/
--- gff2ps-0.98d.orig/debian/watch
+++ gff2ps-0.98d/debian/watch
@@ -0,0 +1,3 @@
+version=3
+
+ftp://genome.imim.es/pub/gff_tools/gff2ps/gff2ps_v(.*).gz debian uupdate
--- gff2ps-0.98d.orig/debian/README.Debian
+++ gff2ps-0.98d/debian/README.Debian
@@ -0,0 +1,9 @@
+gff2ps for Debian
+-----------------
+
+There is an Perl implementation of gff2ps included on Bioperl package, located
+at /usr/share/doc/bioperl/examples/tools/gff2ps.pl.gz
+Note that this Perl program is very basic and limited. Also, it's not a
+ready-to-use application.
+
+ -- Nelson A. de Oliveira <naoliv@gmail.com>, Wed, 01 Jun 2005 18:30:46 -0300
--- gff2ps-0.98d.orig/debian/rules
+++ gff2ps-0.98d/debian/rules
@@ -0,0 +1,8 @@
+#!/usr/bin/make -f
+
+include /usr/share/cdbs/1/rules/simple-patchsys.mk
+include /usr/share/cdbs/1/rules/debhelper.mk
+
+install/gff2ps::
+	install -m 755 gff2ps_v0.98d debian/gff2ps/usr/share/gff2ps/gff2ps.real
+	install -m 644 debian/linda.override debian/gff2ps/usr/share/linda/overrides/gff2ps
--- gff2ps-0.98d.orig/debian/compat
+++ gff2ps-0.98d/debian/compat
@@ -0,0 +1 @@
+5
--- gff2ps-0.98d.orig/debian/wrapper/gff2ps
+++ gff2ps-0.98d/debian/wrapper/gff2ps
@@ -0,0 +1,3 @@
+#!/bin/bash
+
+LC_ALL=C /usr/share/gff2ps/gff2ps.real "$@"
--- gff2ps-0.98d.orig/debian/dirs
+++ gff2ps-0.98d/debian/dirs
@@ -0,0 +1,3 @@
+usr/bin
+usr/share/gff2ps
+usr/share/linda/overrides