[med-svn] r426 - in trunk/packages/wise/trunk: . debian debian/manpages.d debian/patches

pbenner-guest at alioth.debian.org pbenner-guest at alioth.debian.org
Mon Sep 17 07:14:21 UTC 2007


Author: pbenner-guest
Date: 2007-09-17 07:14:21 +0000 (Mon, 17 Sep 2007)
New Revision: 426

Added:
   trunk/packages/wise/trunk/debian/
   trunk/packages/wise/trunk/debian/README.Debian
   trunk/packages/wise/trunk/debian/changelog
   trunk/packages/wise/trunk/debian/compat
   trunk/packages/wise/trunk/debian/control
   trunk/packages/wise/trunk/debian/copyright
   trunk/packages/wise/trunk/debian/dirs
   trunk/packages/wise/trunk/debian/docs
   trunk/packages/wise/trunk/debian/manpages
   trunk/packages/wise/trunk/debian/manpages.d/
   trunk/packages/wise/trunk/debian/manpages.d/Makefile
   trunk/packages/wise/trunk/debian/manpages.d/dba.sgml
   trunk/packages/wise/trunk/debian/manpages.d/dnal.sgml
   trunk/packages/wise/trunk/debian/manpages.d/estwise.sgml
   trunk/packages/wise/trunk/debian/manpages.d/estwisedb.sgml
   trunk/packages/wise/trunk/debian/manpages.d/genewise.sgml
   trunk/packages/wise/trunk/debian/manpages.d/genewisedb.sgml
   trunk/packages/wise/trunk/debian/manpages.d/genomewise.sgml
   trunk/packages/wise/trunk/debian/manpages.d/promoterwise.sgml
   trunk/packages/wise/trunk/debian/manpages.d/psw.sgml
   trunk/packages/wise/trunk/debian/manpages.d/pswdb.sgml
   trunk/packages/wise/trunk/debian/manpages.d/scanwise.sgml
   trunk/packages/wise/trunk/debian/manpages.d/scanwise_server.sgml
   trunk/packages/wise/trunk/debian/patches/
   trunk/packages/wise/trunk/debian/patches/00list
   trunk/packages/wise/trunk/debian/patches/01_welcome-csh.dpatch
   trunk/packages/wise/trunk/debian/patches/02_isnumber.dpatch
   trunk/packages/wise/trunk/debian/patches/03_doc-nodycache.dpatch
   trunk/packages/wise/trunk/debian/patches/04_wise2-pdflatex-update.dpatch
   trunk/packages/wise/trunk/debian/rules
   trunk/packages/wise/trunk/debian/watch
   trunk/packages/wise/trunk/debian/wise-doc.doc-base.api
   trunk/packages/wise/trunk/debian/wise-doc.doc-base.dynamite
   trunk/packages/wise/trunk/debian/wise-doc.doc-base.wise
   trunk/packages/wise/trunk/debian/wise-doc.docs
   trunk/packages/wise/trunk/debian/wise-doc.examples
Log:
[svn-inject] Applying Debian modifications to trunk


Property changes on: trunk/packages/wise/trunk/debian
___________________________________________________________________
Name: mergeWithUpstream
   + 1

Added: trunk/packages/wise/trunk/debian/README.Debian
===================================================================
--- trunk/packages/wise/trunk/debian/README.Debian	                        (rev 0)
+++ trunk/packages/wise/trunk/debian/README.Debian	2007-09-17 07:14:21 UTC (rev 426)
@@ -0,0 +1,7 @@
+wise for Debian
+--------------------------------------------------------------------------------
+
+You may want to copy /usr/share/doc/wise-doc/examles/* (distributed by wise-doc)
+to your home directory and set WISECONFIGDIR appropriately.
+
+ -- Philipp Benner <mail at philipp-benner.de>, Sat, 29 Jul 2006 19:29:53 z

Added: trunk/packages/wise/trunk/debian/changelog
===================================================================
--- trunk/packages/wise/trunk/debian/changelog	                        (rev 0)
+++ trunk/packages/wise/trunk/debian/changelog	2007-09-17 07:14:21 UTC (rev 426)
@@ -0,0 +1,68 @@
+wise (2.4.1-1) unstable; urgency=low
+
+  * New upstream release.
+
+ -- Philipp Benner <mail at philipp-benner.de>  Sat, 15 Sep 2007 17:18:49 +0200
+
+wise (2.4.0-3) unstable; urgency=low
+
+  * Removed debtags from debian/control.
+  * Updated package description (Closes: #435904).
+  * Excluded genewise21.eps and genewise6.eps from documentation
+  + (workaround for a bug in gs-esp).
+
+ -- Philipp Benner <mail at philipp-benner.de>  Sun, 05 Aug 2007 20:21:35 +0200
+
+wise (2.4.0-2) unstable; urgency=low
+
+  * Converted wise2.tex to a pdflatex compatible latex file
+  + (workaround for a bug in dvips)
+
+ -- Philipp Benner <mail at philipp-benner.de>  Fri, 27 Jul 2007 18:46:33 +0200
+
+wise (2.4.0-1) unstable; urgency=low
+
+  * New upstream release (Closes: #431392)
+  * New dpatch (02_isnumber): src/models/phasemodel.c: replaces isnumber() by isdigit()
+  * New dpatch (03_doc-nodycache): docs/wise2.tex: minor bugfix
+
+ -- Philipp Benner <mail at philipp-benner.de>  Tue, 24 Jul 2007 11:58:36 +0200
+
+wise (2.2.0-5) unstable; urgency=low
+
+  * Removed obsolete dependencies (Closes: #422123)
+
+ -- Philipp Benner <mail at philipp-benner.de>  Sun,  6 May 2007 22:42:27 +0200
+
+wise (2.2.0-4) unstable; urgency=low
+
+  * Adapted debian-med tags
+  * Uscan support
+  * Migrating to texlive
+  * use /bin/sh instead of /bin/csh in src/welcome.csh
+
+ -- Philipp Benner <mail at philipp-benner.de>  Tue, 27 Mar 2007 19:29:08 +0200
+
+wise (2.2.0-3) unstable; urgency=low
+
+  * package tags
+  * fixed typos in package description
+
+ -- Philipp Benner <mail at philipp-benner.de>  Thu, 21 Sep 2006 14:22:39 +0200
+
+wise (2.2.0-2) unstable; urgency=low
+
+  * removed \ref tags from package description
+  * moved examples to package wise-doc
+  * fixed typo in README.Debian
+  * minor changes in debian/control
+  * fixed typo in package description (Closes: #380451)
+  * new html documentation
+
+ -- Philipp Benner <mail at philipp-benner.de>  Sun, 30 Jul 2006 14:08:20 +0200
+
+wise (2.2.0-1) unstable; urgency=low
+
+  * Initial release (Closes: #379604)
+
+ -- Philipp Benner <mail at philipp-benner.de>  Sun, 23 Jul 2006 17:29:49 +0200

Added: trunk/packages/wise/trunk/debian/compat
===================================================================
--- trunk/packages/wise/trunk/debian/compat	                        (rev 0)
+++ trunk/packages/wise/trunk/debian/compat	2007-09-17 07:14:21 UTC (rev 426)
@@ -0,0 +1 @@
+5

Added: trunk/packages/wise/trunk/debian/control
===================================================================
--- trunk/packages/wise/trunk/debian/control	                        (rev 0)
+++ trunk/packages/wise/trunk/debian/control	2007-09-17 07:14:21 UTC (rev 426)
@@ -0,0 +1,67 @@
+Source: wise
+Section: science
+Priority: optional
+Maintainer: Philipp Benner <mail at philipp-benner.de>
+Build-Depends: debhelper (>= 5), dpatch (>= 2.0.21), texlive-latex-base,
+ texlive-extra-utils, hevea, docbook-to-man, libglib1.2-dev
+Standards-Version: 3.7.2.1
+
+Package: wise
+Architecture: any
+Depends: ${shlibs:Depends}
+Recommends: wise-doc (= ${source:Version})
+Description: comparison of biopolymers, commonly DNA and protein sequences
+ Wise2 is a package focused on comparisons of biopolymers, commonly DNA
+ and protein sequences. There are many other packages which do
+ this, probably the best known being BLAST package (from NCBI) and the 
+ Fasta package (from Bill Pearson). There are other packages, such as
+ the HMMER package (Sean Eddy) or SAM package (UC Santa Cruz) focused
+ on hidden Markov models (HMMs) of biopolymers.
+ .
+ Wise2's particular forte is the comparison of DNA sequence at the level
+ of its protein translation. This comparison allows the simultaneous
+ prediction of say gene structure with homology based alignment.
+ .
+ Wise2 also contains other algorithms, such as the venerable Smith-Waterman
+ algorithm, or more modern ones such as Stephen Altschul's generalised
+ gap penalties, or even experimental ones developed in house, such as
+ dba. The development of these algorithms is due to the ease of developing
+ such algorithms in the enviroment used by Wise2. 
+ .
+ Wise2 has also been written with an eye for reuse and maintainability. 
+ Although it is a pure C package you can access its functionality 
+ directly in Perl. Parts of the package (or the entire package) can
+ be used by other C or C++ programs without namespace clashes as all
+ externally linked variables have the unique identifier Wise2 prepended.
+ .
+  Homepage: http://www.ebi.ac.uk/~birney/wise2/
+
+Package: wise-doc
+Architecture: all
+Section: doc
+Recommends: wise (= ${source:Version}), xpdf-reader | pdf-viewer
+Description: documentation for the wise package
+ Wise2 is a package focused on comparisons of biopolymers, commonly DNA
+ and protein sequences. There are many other packages which do
+ this, probably the best known being BLAST package (from NCBI) and the 
+ Fasta package (from Bill Pearson). There are other packages, such as
+ the HMMER package (Sean Eddy) or SAM package (UC Santa Cruz) focused
+ on hidden Markov models (HMMs) of biopolymers.
+ .
+ Wise2's particular forte is the comparison of DNA sequence at the level
+ of its protein translation. This comparison allows the simultaneous
+ prediction of say gene structure with homology based alignment.
+ .
+ Wise2 also contains other algorithms, such as the venerable Smith-Waterman
+ algorithm, or more modern ones such as Stephen Altschul's generalised
+ gap penalties, or even experimental ones developed in house, such as
+ dba. The development of these algorithms is due to the ease of developing
+ such algorithms in the enviroment used by Wise2. 
+ .
+ Wise2 has also been written with an eye for reuse and maintainability. 
+ Although it is a pure C package you can access its functionality 
+ directly in Perl. Parts of the package (or the entire package) can
+ be used by other C or C++ programs without namespace clashes as all
+ externally linked variables have the unique identifier Wise2 prepended.
+ .
+  Homepage: http://www.ebi.ac.uk/~birney/wise2/

Added: trunk/packages/wise/trunk/debian/copyright
===================================================================
--- trunk/packages/wise/trunk/debian/copyright	                        (rev 0)
+++ trunk/packages/wise/trunk/debian/copyright	2007-09-17 07:14:21 UTC (rev 426)
@@ -0,0 +1,65 @@
+This package was debianized by Philipp Benner <mail at philipp-benner.de> on
+Sun, 23 Jul 2006 17:29:49 +0200.
+
+It was downloaded from ftp://ftp.ebi.ac.uk/pub/software/unix/wise2/
+
+Upstream Author: Ewan Birney <birney at ebi.ac.uk>
+
+Copyright:
+	1996, 1998, 1999, 2001
+	Ewan Birney, birney at sanger.ac.uk
+	Richard Copley
+	Sean Eddy
+
+License:
+
+GPL (see /usr/share/common-licenses/GPL)
+
+
+The Debian packaging is (C) 2006, Philipp Benner <mail at philipp-benner.de> and
+is licensed under the GPL, see `/usr/share/common-licenses/GPL'.
+
+
+License for dynlibsrc:
+
+All of the documentation and software included in the dynlibsrc
+directory of the Wise2 package directory is copyrighted by Genome
+Research Limited (GRL) and other individuals where appropriate. This
+license is modelled after the 'BSD' style license and is appropriate
+for use by both academic and commericial sites, without placing any
+restriction on the distribution of source code from other sources with
+this software.
+
+Copyright 1998, 1999, GRL and others.
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are
+met:
+
+  1.Redistributions of source code must retain the above copyright
+    notice, this list of conditions and the following disclaimer.
+
+  2.Redistributions in binary form must reproduce the above copyright
+    notice, this list of conditions and the following disclaimer in
+    the documentation and/or other materials provided with the
+    distribution.
+
+  3.Neither the name GRL nor the names of its contributors may be used
+    to endorse or promote products derived from this software without
+    specific prior written permission.
+
+It is considered polite to indicate where appropriate that software which
+is developed using this source code includes a statement that it was developed
+using the Wise2 soure code. This is not a requirement however.
+
+THIS SOFTWARE IS PROVIDED BY THE GRL AND CONTRIBUTORS ``AS IS'' AND
+ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE GRL OR CONTRIBUTORS BE
+LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
+CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
+SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR
+BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE
+OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN
+IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

Added: trunk/packages/wise/trunk/debian/dirs
===================================================================
--- trunk/packages/wise/trunk/debian/dirs	                        (rev 0)
+++ trunk/packages/wise/trunk/debian/dirs	2007-09-17 07:14:21 UTC (rev 426)
@@ -0,0 +1 @@
+usr/bin

Added: trunk/packages/wise/trunk/debian/docs
===================================================================
--- trunk/packages/wise/trunk/debian/docs	                        (rev 0)
+++ trunk/packages/wise/trunk/debian/docs	2007-09-17 07:14:21 UTC (rev 426)
@@ -0,0 +1 @@
+README

Added: trunk/packages/wise/trunk/debian/manpages
===================================================================
--- trunk/packages/wise/trunk/debian/manpages	                        (rev 0)
+++ trunk/packages/wise/trunk/debian/manpages	2007-09-17 07:14:21 UTC (rev 426)
@@ -0,0 +1,12 @@
+debian/manpages.d/dba.1
+debian/manpages.d/dnal.1
+debian/manpages.d/estwise.1
+debian/manpages.d/estwisedb.1
+debian/manpages.d/genewise.1
+debian/manpages.d/genewisedb.1
+debian/manpages.d/genomewise.1
+debian/manpages.d/promoterwise.1
+debian/manpages.d/psw.1
+debian/manpages.d/pswdb.1
+debian/manpages.d/scanwise.1
+debian/manpages.d/scanwise_server.1

Added: trunk/packages/wise/trunk/debian/manpages.d/Makefile
===================================================================
--- trunk/packages/wise/trunk/debian/manpages.d/Makefile	                        (rev 0)
+++ trunk/packages/wise/trunk/debian/manpages.d/Makefile	2007-09-17 07:14:21 UTC (rev 426)
@@ -0,0 +1,13 @@
+SHELL		= /bin/sh
+
+MANPAGES	= dba.1 dnal.1 estwise.1 estwisedb.1 genewise.1 genewisedb.1 genomewise.1 promoterwise.1 psw.1 pswdb.1 scanwise.1 scanwise_server.1
+
+all: $(MANPAGES)
+
+$(MANPAGES): %.1 : %.sgml
+	docbook-to-man $< > $@
+
+clean:
+	$(RM) $(MANPAGES)
+
+.PHONY: all

Added: trunk/packages/wise/trunk/debian/manpages.d/dba.sgml
===================================================================
--- trunk/packages/wise/trunk/debian/manpages.d/dba.sgml	                        (rev 0)
+++ trunk/packages/wise/trunk/debian/manpages.d/dba.sgml	2007-09-17 07:14:21 UTC (rev 426)
@@ -0,0 +1,155 @@
+<!doctype refentry PUBLIC "-//OASIS//DTD DocBook V4.1//EN" [
+
+<!-- Process this file with docbook-to-man to generate an nroff manual
+     page: `docbook-to-man manpage.sgml > manpage.1'.  You may view
+     the manual page with: `docbook-to-man manpage.sgml | nroff -man |
+     less'.  A typical entry in a Makefile or Makefile.am is:
+
+manpage.1: manpage.sgml
+	docbook-to-man $< > $@
+
+    
+	The docbook-to-man binary is found in the docbook-to-man package.
+	Please remember that if you create the nroff version in one of the
+	debian/rules file targets (such as build), you will need to include
+	docbook-to-man in your Build-Depends control field.
+
+  -->
+
+
+  <!-- Fill in your name for FIRSTNAME and SURNAME. -->
+  <!ENTITY dhfirstname "<firstname>Philipp</firstname>">
+  <!ENTITY dhsurname   "<surname>Benner</surname>">
+  <!-- Please adjust the date whenever revising the manpage. -->
+  <!ENTITY dhdate      "<date>July 2006</date>">
+  <!-- SECTION should be 1-8, maybe w/ subsection other parameters are
+       allowed: see man(7), man(1). -->
+  <!ENTITY dhsection   "<manvolnum>1</manvolnum>">
+  <!ENTITY dhemail     "<email>mail at philipp-benner.de</email>">
+  <!ENTITY dhusername  "Philipp Benner">
+  <!ENTITY dhucpackage "<refentrytitle>DBA</refentrytitle>">
+  <!ENTITY dhpackage   "dba">
+
+  <!ENTITY debian      "<productname>Debian</productname>">
+  <!ENTITY gnu         "<acronym>GNU</acronym>">
+  <!ENTITY gpl         "&gnu; <acronym>GPL</acronym>">
+]>
+
+<refentry>
+  <refentryinfo>
+    <address>
+      &dhemail;
+    </address>
+    <author>
+      &dhfirstname;
+      &dhsurname;
+    </author>
+    <copyright>
+      <year>2006</year>
+      <holder>&dhusername;</holder>
+    </copyright>
+    &dhdate;
+  </refentryinfo>
+  <refmeta>
+    &dhucpackage;
+
+    &dhsection;
+  </refmeta>
+  <refnamediv>
+    <refname>&dhpackage;</refname>
+
+    <refpurpose>characterising shared regulatory regions of genomic DNA</refpurpose>
+  </refnamediv>
+  <refsynopsisdiv>
+    <cmdsynopsis>
+      <command>&dhpackage;</command>
+
+      <group choice=opt>
+        <arg rep=repeat><replaceable>options</replaceable></arg>
+      </group>
+
+      <group choice=req>
+<!-- 	<arg rep=repeat><replaceable>seq1</replaceable></arg> -->
+<!-- 	<arg rep=repeat><replaceable>seq2</replaceable></arg> -->
+	<arg><replaceable> seq1 seq2</replaceable></arg>
+      </group>
+
+    </cmdsynopsis>
+  </refsynopsisdiv>
+  <refsect1>
+    <title>DESCRIPTION</title>
+
+    <para>dba - standing for Dna Block Aligner, was developped by Niclas Jareborg,
+    Richard Durbin and Ewan Birney for characterising shared regulatory regions
+    of genomic DNA, either in upstream regions or introns of genes</para>
+
+    <para>The idea was that in these regions there would a series of shared motifs,
+    perhaps with one or two insertions or deletions but between motifs there
+    would be any length of sequence.</para>
+    
+    <para>The subsquent model was a 3 state model which was log-odd'd ratio to a null
+    model of their being no examples of a motif in the two sequences.</para>
+
+  </refsect1>
+  <refsect1>
+    <title>OPTIONS</title>
+
+    <variablelist>
+      <varlistentry>
+        <term><option>-h</option>
+          <option>-help</option>
+        </term>
+        <listitem>
+          <para>Show summary of options.</para>
+        </listitem>
+      </varlistentry>
+      <varlistentry>
+        <term><option>-v</option>
+          <option>-version</option>
+        </term>
+        <listitem>
+          <para>Show version of program.</para>
+        </listitem>
+      </varlistentry>
+    </variablelist>
+  </refsect1>
+  <refsect1>
+    <title>SEE ALSO</title>
+
+    <para>dnal (1), estwise (1), estwisedb (1), genewise (1), genewisedb (1), genomewise (1), promoterwise (1), psw (1), pswdb (1), scanwise (1), scanwise_server (1).</para>
+  </refsect1>
+  <refsect1>
+    <title>AUTHOR</title>
+
+    <para>This manual page was written by &dhusername; &dhemail; for
+      the &debian; system (but may be used by others).  Permission is
+      granted to copy, distribute and/or modify this document under
+      the terms of the &gnu; General Public License, Version 2 any 
+      later version published by the Free Software Foundation.
+    </para>
+    <para>
+      On Debian systems, the complete text of the GNU General Public
+      License can be found in /usr/share/common-licenses/GPL.
+    </para>
+
+  </refsect1>
+</refentry>
+
+<!-- Keep this comment at the end of the file
+Local variables:
+mode: sgml
+sgml-omittag:t
+sgml-shorttag:t
+sgml-minimize-attributes:nil
+sgml-always-quote-attributes:t
+sgml-indent-step:2
+sgml-indent-data:t
+sgml-parent-document:nil
+sgml-default-dtd-file:nil
+sgml-exposed-tags:nil
+sgml-local-catalogs:nil
+sgml-local-ecat-files:nil
+End:
+-->
+
+

Added: trunk/packages/wise/trunk/debian/manpages.d/dnal.sgml
===================================================================
--- trunk/packages/wise/trunk/debian/manpages.d/dnal.sgml	                        (rev 0)
+++ trunk/packages/wise/trunk/debian/manpages.d/dnal.sgml	2007-09-17 07:14:21 UTC (rev 426)
@@ -0,0 +1,144 @@
+<!doctype refentry PUBLIC "-//OASIS//DTD DocBook V4.1//EN" [
+
+<!-- Process this file with docbook-to-man to generate an nroff manual
+     page: `docbook-to-man manpage.sgml > manpage.1'.  You may view
+     the manual page with: `docbook-to-man manpage.sgml | nroff -man |
+     less'.  A typical entry in a Makefile or Makefile.am is:
+
+manpage.1: manpage.sgml
+	docbook-to-man $< > $@
+
+    
+	The docbook-to-man binary is found in the docbook-to-man package.
+	Please remember that if you create the nroff version in one of the
+	debian/rules file targets (such as build), you will need to include
+	docbook-to-man in your Build-Depends control field.
+
+  -->
+
+
+  <!-- Fill in your name for FIRSTNAME and SURNAME. -->
+  <!ENTITY dhfirstname "<firstname>Philipp</firstname>">
+  <!ENTITY dhsurname   "<surname>Benner</surname>">
+  <!-- Please adjust the date whenever revising the manpage. -->
+  <!ENTITY dhdate      "<date>July 2006</date>">
+  <!-- SECTION should be 1-8, maybe w/ subsection other parameters are
+       allowed: see man(7), man(1). -->
+  <!ENTITY dhsection   "<manvolnum>1</manvolnum>">
+  <!ENTITY dhemail     "<email>mail at philipp-benner.de</email>">
+  <!ENTITY dhusername  "Philipp Benner">
+  <!ENTITY dhucpackage "<refentrytitle>DNAL</refentrytitle>">
+  <!ENTITY dhpackage   "dnal">
+
+  <!ENTITY debian      "<productname>Debian</productname>">
+  <!ENTITY gnu         "<acronym>GNU</acronym>">
+  <!ENTITY gpl         "&gnu; <acronym>GPL</acronym>">
+]>
+
+<refentry>
+  <refentryinfo>
+    <address>
+      &dhemail;
+    </address>
+    <author>
+      &dhfirstname;
+      &dhsurname;
+    </author>
+    <copyright>
+      <year>2006</year>
+      <holder>&dhusername;</holder>
+    </copyright>
+    &dhdate;
+  </refentryinfo>
+  <refmeta>
+    &dhucpackage;
+
+    &dhsection;
+  </refmeta>
+  <refnamediv>
+    <refname>&dhpackage;</refname>
+
+    <refpurpose>...</refpurpose>
+  </refnamediv>
+  <refsynopsisdiv>
+    <cmdsynopsis>
+      <command>&dhpackage;</command>
+
+      <group choice=opt>
+        <arg rep=repeat><replaceable>options</replaceable></arg>
+      </group>
+
+      <group choice=req>
+<!-- 	<arg rep=repeat><replaceable>seq1</replaceable></arg> -->
+<!-- 	<arg rep=repeat><replaceable>seq2</replaceable></arg> -->
+	<arg><replaceable> dna-file dna-file</replaceable></arg>
+      </group>
+
+    </cmdsynopsis>
+  </refsynopsisdiv>
+  <refsect1>
+    <title>DESCRIPTION</title>
+
+    <para>not available</para>
+
+  </refsect1>
+  <refsect1>
+    <title>OPTIONS</title>
+
+    <variablelist>
+      <varlistentry>
+        <term><option>-help</option>
+        </term>
+        <listitem>
+          <para>Show summary of options.</para>
+        </listitem>
+      </varlistentry>
+      <varlistentry>
+        <term><option>-version</option>
+        </term>
+        <listitem>
+          <para>Show version of program.</para>
+        </listitem>
+      </varlistentry>
+    </variablelist>
+  </refsect1>
+  <refsect1>
+    <title>SEE ALSO</title>
+
+    <para>dba (1), estwise (1), estwisedb (1), genewise (1), genewisedb (1), genomewise (1), promoterwise (1), psw (1), pswdb (1), scanwise (1), scanwise_server (1).</para>
+  </refsect1>
+  <refsect1>
+    <title>AUTHOR</title>
+
+    <para>This manual page was written by &dhusername; &dhemail; for
+      the &debian; system (but may be used by others).  Permission is
+      granted to copy, distribute and/or modify this document under
+      the terms of the &gnu; General Public License, Version 2 any 
+      later version published by the Free Software Foundation.
+    </para>
+    <para>
+      On Debian systems, the complete text of the GNU General Public
+      License can be found in /usr/share/common-licenses/GPL.
+    </para>
+
+  </refsect1>
+</refentry>
+
+<!-- Keep this comment at the end of the file
+Local variables:
+mode: sgml
+sgml-omittag:t
+sgml-shorttag:t
+sgml-minimize-attributes:nil
+sgml-always-quote-attributes:t
+sgml-indent-step:2
+sgml-indent-data:t
+sgml-parent-document:nil
+sgml-default-dtd-file:nil
+sgml-exposed-tags:nil
+sgml-local-catalogs:nil
+sgml-local-ecat-files:nil
+End:
+-->
+
+

Added: trunk/packages/wise/trunk/debian/manpages.d/estwise.sgml
===================================================================
--- trunk/packages/wise/trunk/debian/manpages.d/estwise.sgml	                        (rev 0)
+++ trunk/packages/wise/trunk/debian/manpages.d/estwise.sgml	2007-09-17 07:14:21 UTC (rev 426)
@@ -0,0 +1,144 @@
+<!doctype refentry PUBLIC "-//OASIS//DTD DocBook V4.1//EN" [
+
+<!-- Process this file with docbook-to-man to generate an nroff manual
+     page: `docbook-to-man manpage.sgml > manpage.1'.  You may view
+     the manual page with: `docbook-to-man manpage.sgml | nroff -man |
+     less'.  A typical entry in a Makefile or Makefile.am is:
+
+manpage.1: manpage.sgml
+	docbook-to-man $< > $@
+
+    
+	The docbook-to-man binary is found in the docbook-to-man package.
+	Please remember that if you create the nroff version in one of the
+	debian/rules file targets (such as build), you will need to include
+	docbook-to-man in your Build-Depends control field.
+
+  -->
+
+
+  <!-- Fill in your name for FIRSTNAME and SURNAME. -->
+  <!ENTITY dhfirstname "<firstname>Philipp</firstname>">
+  <!ENTITY dhsurname   "<surname>Benner</surname>">
+  <!-- Please adjust the date whenever revising the manpage. -->
+  <!ENTITY dhdate      "<date>July 2006</date>">
+  <!-- SECTION should be 1-8, maybe w/ subsection other parameters are
+       allowed: see man(7), man(1). -->
+  <!ENTITY dhsection   "<manvolnum>1</manvolnum>">
+  <!ENTITY dhemail     "<email>mail at philipp-benner.de</email>">
+  <!ENTITY dhusername  "Philipp Benner">
+  <!ENTITY dhucpackage "<refentrytitle>ESTWISE</refentrytitle>">
+  <!ENTITY dhpackage   "estwise">
+
+  <!ENTITY debian      "<productname>Debian</productname>">
+  <!ENTITY gnu         "<acronym>GNU</acronym>">
+  <!ENTITY gpl         "&gnu; <acronym>GPL</acronym>">
+]>
+
+<refentry>
+  <refentryinfo>
+    <address>
+      &dhemail;
+    </address>
+    <author>
+      &dhfirstname;
+      &dhsurname;
+    </author>
+    <copyright>
+      <year>2006</year>
+      <holder>&dhusername;</holder>
+    </copyright>
+    &dhdate;
+  </refentryinfo>
+  <refmeta>
+    &dhucpackage;
+
+    &dhsection;
+  </refmeta>
+  <refnamediv>
+    <refname>&dhpackage;</refname>
+
+    <refpurpose>comparison of a related protein to cDNA (or ESTs)</refpurpose>
+  </refnamediv>
+  <refsynopsisdiv>
+    <cmdsynopsis>
+      <command>&dhpackage;</command>
+
+      <group choice=opt>
+        <arg rep=repeat><replaceable>options</replaceable></arg>
+      </group>
+
+      <group choice=req>
+<!-- 	<arg rep=repeat><replaceable>seq1</replaceable></arg> -->
+<!-- 	<arg rep=repeat><replaceable>seq2</replaceable></arg> -->
+	<arg><replaceable> protein-file dna-file</replaceable></arg>
+      </group>
+
+    </cmdsynopsis>
+  </refsynopsisdiv>
+  <refsect1>
+    <title>DESCRIPTION</title>
+
+    <para>not available</para>
+
+  </refsect1>
+  <refsect1>
+    <title>OPTIONS</title>
+
+    <variablelist>
+      <varlistentry>
+        <term><option>-help</option>
+        </term>
+        <listitem>
+          <para>Show summary of options.</para>
+        </listitem>
+      </varlistentry>
+      <varlistentry>
+        <term><option>-version</option>
+        </term>
+        <listitem>
+          <para>Show version of program.</para>
+        </listitem>
+      </varlistentry>
+    </variablelist>
+  </refsect1>
+  <refsect1>
+    <title>SEE ALSO</title>
+
+    <para>dba (1), dnal (1), estwisedb (1), genewise (1), genewisedb (1), genomewise (1), promoterwise (1), psw (1), pswdb (1), scanwise (1), scanwise_server (1).</para>
+  </refsect1>
+  <refsect1>
+    <title>AUTHOR</title>
+
+    <para>This manual page was written by &dhusername; &dhemail; for
+      the &debian; system (but may be used by others).  Permission is
+      granted to copy, distribute and/or modify this document under
+      the terms of the &gnu; General Public License, Version 2 any 
+      later version published by the Free Software Foundation.
+    </para>
+    <para>
+      On Debian systems, the complete text of the GNU General Public
+      License can be found in /usr/share/common-licenses/GPL.
+    </para>
+
+  </refsect1>
+</refentry>
+
+<!-- Keep this comment at the end of the file
+Local variables:
+mode: sgml
+sgml-omittag:t
+sgml-shorttag:t
+sgml-minimize-attributes:nil
+sgml-always-quote-attributes:t
+sgml-indent-step:2
+sgml-indent-data:t
+sgml-parent-document:nil
+sgml-default-dtd-file:nil
+sgml-exposed-tags:nil
+sgml-local-catalogs:nil
+sgml-local-ecat-files:nil
+End:
+-->
+
+

Added: trunk/packages/wise/trunk/debian/manpages.d/estwisedb.sgml
===================================================================
--- trunk/packages/wise/trunk/debian/manpages.d/estwisedb.sgml	                        (rev 0)
+++ trunk/packages/wise/trunk/debian/manpages.d/estwisedb.sgml	2007-09-17 07:14:21 UTC (rev 426)
@@ -0,0 +1,144 @@
+<!doctype refentry PUBLIC "-//OASIS//DTD DocBook V4.1//EN" [
+
+<!-- Process this file with docbook-to-man to generate an nroff manual
+     page: `docbook-to-man manpage.sgml > manpage.1'.  You may view
+     the manual page with: `docbook-to-man manpage.sgml | nroff -man |
+     less'.  A typical entry in a Makefile or Makefile.am is:
+
+manpage.1: manpage.sgml
+	docbook-to-man $< > $@
+
+    
+	The docbook-to-man binary is found in the docbook-to-man package.
+	Please remember that if you create the nroff version in one of the
+	debian/rules file targets (such as build), you will need to include
+	docbook-to-man in your Build-Depends control field.
+
+  -->
+
+
+  <!-- Fill in your name for FIRSTNAME and SURNAME. -->
+  <!ENTITY dhfirstname "<firstname>Philipp</firstname>">
+  <!ENTITY dhsurname   "<surname>Benner</surname>">
+  <!-- Please adjust the date whenever revising the manpage. -->
+  <!ENTITY dhdate      "<date>July 2006</date>">
+  <!-- SECTION should be 1-8, maybe w/ subsection other parameters are
+       allowed: see man(7), man(1). -->
+  <!ENTITY dhsection   "<manvolnum>1</manvolnum>">
+  <!ENTITY dhemail     "<email>mail at philipp-benner.de</email>">
+  <!ENTITY dhusername  "Philipp Benner">
+  <!ENTITY dhucpackage "<refentrytitle>ESTWISEDB</refentrytitle>">
+  <!ENTITY dhpackage   "estwisedb">
+
+  <!ENTITY debian      "<productname>Debian</productname>">
+  <!ENTITY gnu         "<acronym>GNU</acronym>">
+  <!ENTITY gpl         "&gnu; <acronym>GPL</acronym>">
+]>
+
+<refentry>
+  <refentryinfo>
+    <address>
+      &dhemail;
+    </address>
+    <author>
+      &dhfirstname;
+      &dhsurname;
+    </author>
+    <copyright>
+      <year>2006</year>
+      <holder>&dhusername;</holder>
+    </copyright>
+    &dhdate;
+  </refentryinfo>
+  <refmeta>
+    &dhucpackage;
+
+    &dhsection;
+  </refmeta>
+  <refnamediv>
+    <refname>&dhpackage;</refname>
+
+    <refpurpose>a database of proteins vs a database of EST/cDNA sequences</refpurpose>
+  </refnamediv>
+  <refsynopsisdiv>
+    <cmdsynopsis>
+      <command>&dhpackage;</command>
+
+      <group choice=opt>
+        <arg rep=repeat><replaceable>options</replaceable></arg>
+      </group>
+
+      <group choice=req>
+<!-- 	<arg rep=repeat><replaceable>seq1</replaceable></arg> -->
+<!-- 	<arg rep=repeat><replaceable>seq2</replaceable></arg> -->
+	<arg><replaceable> protein-input dna-input</replaceable></arg>
+      </group>
+
+    </cmdsynopsis>
+  </refsynopsisdiv>
+  <refsect1>
+    <title>DESCRIPTION</title>
+
+    <para>not available</para>
+
+  </refsect1>
+  <refsect1>
+    <title>OPTIONS</title>
+
+    <variablelist>
+      <varlistentry>
+        <term><option>-help</option>
+        </term>
+        <listitem>
+          <para>Show summary of options.</para>
+        </listitem>
+      </varlistentry>
+      <varlistentry>
+        <term><option>-version</option>
+        </term>
+        <listitem>
+          <para>Show version of program.</para>
+        </listitem>
+      </varlistentry>
+    </variablelist>
+  </refsect1>
+  <refsect1>
+    <title>SEE ALSO</title>
+
+    <para>dba (1), dnal (1), estwise (1), genewise (1), genewisedb (1), genomewise (1), promoterwise (1), psw (1), pswdb (1), scanwise (1), scanwise_server (1).</para>
+  </refsect1>
+  <refsect1>
+    <title>AUTHOR</title>
+
+    <para>This manual page was written by &dhusername; &dhemail; for
+      the &debian; system (but may be used by others).  Permission is
+      granted to copy, distribute and/or modify this document under
+      the terms of the &gnu; General Public License, Version 2 any 
+      later version published by the Free Software Foundation.
+    </para>
+    <para>
+      On Debian systems, the complete text of the GNU General Public
+      License can be found in /usr/share/common-licenses/GPL.
+    </para>
+
+  </refsect1>
+</refentry>
+
+<!-- Keep this comment at the end of the file
+Local variables:
+mode: sgml
+sgml-omittag:t
+sgml-shorttag:t
+sgml-minimize-attributes:nil
+sgml-always-quote-attributes:t
+sgml-indent-step:2
+sgml-indent-data:t
+sgml-parent-document:nil
+sgml-default-dtd-file:nil
+sgml-exposed-tags:nil
+sgml-local-catalogs:nil
+sgml-local-ecat-files:nil
+End:
+-->
+
+

Added: trunk/packages/wise/trunk/debian/manpages.d/genewise.sgml
===================================================================
--- trunk/packages/wise/trunk/debian/manpages.d/genewise.sgml	                        (rev 0)
+++ trunk/packages/wise/trunk/debian/manpages.d/genewise.sgml	2007-09-17 07:14:21 UTC (rev 426)
@@ -0,0 +1,144 @@
+<!doctype refentry PUBLIC "-//OASIS//DTD DocBook V4.1//EN" [
+
+<!-- Process this file with docbook-to-man to generate an nroff manual
+     page: `docbook-to-man manpage.sgml > manpage.1'.  You may view
+     the manual page with: `docbook-to-man manpage.sgml | nroff -man |
+     less'.  A typical entry in a Makefile or Makefile.am is:
+
+manpage.1: manpage.sgml
+	docbook-to-man $< > $@
+
+    
+	The docbook-to-man binary is found in the docbook-to-man package.
+	Please remember that if you create the nroff version in one of the
+	debian/rules file targets (such as build), you will need to include
+	docbook-to-man in your Build-Depends control field.
+
+  -->
+
+
+  <!-- Fill in your name for FIRSTNAME and SURNAME. -->
+  <!ENTITY dhfirstname "<firstname>Philipp</firstname>">
+  <!ENTITY dhsurname   "<surname>Benner</surname>">
+  <!-- Please adjust the date whenever revising the manpage. -->
+  <!ENTITY dhdate      "<date>July 2006</date>">
+  <!-- SECTION should be 1-8, maybe w/ subsection other parameters are
+       allowed: see man(7), man(1). -->
+  <!ENTITY dhsection   "<manvolnum>1</manvolnum>">
+  <!ENTITY dhemail     "<email>mail at philipp-benner.de</email>">
+  <!ENTITY dhusername  "Philipp Benner">
+  <!ENTITY dhucpackage "<refentrytitle>GENEWISE</refentrytitle>">
+  <!ENTITY dhpackage   "genewise">
+
+  <!ENTITY debian      "<productname>Debian</productname>">
+  <!ENTITY gnu         "<acronym>GNU</acronym>">
+  <!ENTITY gpl         "&gnu; <acronym>GPL</acronym>">
+]>
+
+<refentry>
+  <refentryinfo>
+    <address>
+      &dhemail;
+    </address>
+    <author>
+      &dhfirstname;
+      &dhsurname;
+    </author>
+    <copyright>
+      <year>2006</year>
+      <holder>&dhusername;</holder>
+    </copyright>
+    &dhdate;
+  </refentryinfo>
+  <refmeta>
+    &dhucpackage;
+
+    &dhsection;
+  </refmeta>
+  <refnamediv>
+    <refname>&dhpackage;</refname>
+
+    <refpurpose>comparison of a related protein to genomic DNA</refpurpose>
+  </refnamediv>
+  <refsynopsisdiv>
+    <cmdsynopsis>
+      <command>&dhpackage;</command>
+
+      <group choice=opt>
+        <arg rep=repeat><replaceable>options</replaceable></arg>
+      </group>
+
+      <group choice=req>
+<!-- 	<arg rep=repeat><replaceable>seq1</replaceable></arg> -->
+<!-- 	<arg rep=repeat><replaceable>seq2</replaceable></arg> -->
+	<arg><replaceable> protein-file dna-file</replaceable></arg>
+      </group>
+
+    </cmdsynopsis>
+  </refsynopsisdiv>
+  <refsect1>
+    <title>DESCRIPTION</title>
+
+    <para>not available</para>
+
+  </refsect1>
+  <refsect1>
+    <title>OPTIONS</title>
+
+    <variablelist>
+      <varlistentry>
+        <term><option>-help</option>
+        </term>
+        <listitem>
+          <para>Show summary of options.</para>
+        </listitem>
+      </varlistentry>
+      <varlistentry>
+        <term><option>-version</option>
+        </term>
+        <listitem>
+          <para>Show version of program.</para>
+        </listitem>
+      </varlistentry>
+    </variablelist>
+  </refsect1>
+  <refsect1>
+    <title>SEE ALSO</title>
+
+    <para>dba (1), dnal (1), estwise (1), estwisedb (1), genewisedb (1), genomewise (1), promoterwise (1), psw (1), pswdb (1), scanwise (1), scanwise_server (1).</para>
+  </refsect1>
+  <refsect1>
+    <title>AUTHOR</title>
+
+    <para>This manual page was written by &dhusername; &dhemail; for
+      the &debian; system (but may be used by others).  Permission is
+      granted to copy, distribute and/or modify this document under
+      the terms of the &gnu; General Public License, Version 2 any 
+      later version published by the Free Software Foundation.
+    </para>
+    <para>
+      On Debian systems, the complete text of the GNU General Public
+      License can be found in /usr/share/common-licenses/GPL.
+    </para>
+
+  </refsect1>
+</refentry>
+
+<!-- Keep this comment at the end of the file
+Local variables:
+mode: sgml
+sgml-omittag:t
+sgml-shorttag:t
+sgml-minimize-attributes:nil
+sgml-always-quote-attributes:t
+sgml-indent-step:2
+sgml-indent-data:t
+sgml-parent-document:nil
+sgml-default-dtd-file:nil
+sgml-exposed-tags:nil
+sgml-local-catalogs:nil
+sgml-local-ecat-files:nil
+End:
+-->
+
+

Added: trunk/packages/wise/trunk/debian/manpages.d/genewisedb.sgml
===================================================================
--- trunk/packages/wise/trunk/debian/manpages.d/genewisedb.sgml	                        (rev 0)
+++ trunk/packages/wise/trunk/debian/manpages.d/genewisedb.sgml	2007-09-17 07:14:21 UTC (rev 426)
@@ -0,0 +1,144 @@
+<!doctype refentry PUBLIC "-//OASIS//DTD DocBook V4.1//EN" [
+
+<!-- Process this file with docbook-to-man to generate an nroff manual
+     page: `docbook-to-man manpage.sgml > manpage.1'.  You may view
+     the manual page with: `docbook-to-man manpage.sgml | nroff -man |
+     less'.  A typical entry in a Makefile or Makefile.am is:
+
+manpage.1: manpage.sgml
+	docbook-to-man $< > $@
+
+    
+	The docbook-to-man binary is found in the docbook-to-man package.
+	Please remember that if you create the nroff version in one of the
+	debian/rules file targets (such as build), you will need to include
+	docbook-to-man in your Build-Depends control field.
+
+  -->
+
+
+  <!-- Fill in your name for FIRSTNAME and SURNAME. -->
+  <!ENTITY dhfirstname "<firstname>Philipp</firstname>">
+  <!ENTITY dhsurname   "<surname>Benner</surname>">
+  <!-- Please adjust the date whenever revising the manpage. -->
+  <!ENTITY dhdate      "<date>July 2006</date>">
+  <!-- SECTION should be 1-8, maybe w/ subsection other parameters are
+       allowed: see man(7), man(1). -->
+  <!ENTITY dhsection   "<manvolnum>1</manvolnum>">
+  <!ENTITY dhemail     "<email>mail at philipp-benner.de</email>">
+  <!ENTITY dhusername  "Philipp Benner">
+  <!ENTITY dhucpackage "<refentrytitle>GENEWISEDB</refentrytitle>">
+  <!ENTITY dhpackage   "genewise">
+
+  <!ENTITY debian      "<productname>Debian</productname>">
+  <!ENTITY gnu         "<acronym>GNU</acronym>">
+  <!ENTITY gpl         "&gnu; <acronym>GPL</acronym>">
+]>
+
+<refentry>
+  <refentryinfo>
+    <address>
+      &dhemail;
+    </address>
+    <author>
+      &dhfirstname;
+      &dhsurname;
+    </author>
+    <copyright>
+      <year>2006</year>
+      <holder>&dhusername;</holder>
+    </copyright>
+    &dhdate;
+  </refentryinfo>
+  <refmeta>
+    &dhucpackage;
+
+    &dhsection;
+  </refmeta>
+  <refnamediv>
+    <refname>&dhpackage;</refname>
+
+    <refpurpose>a database of proteins vs a database of genomic dna sequences</refpurpose>
+  </refnamediv>
+  <refsynopsisdiv>
+    <cmdsynopsis>
+      <command>&dhpackage;</command>
+
+      <group choice=opt>
+        <arg rep=repeat><replaceable>options</replaceable></arg>
+      </group>
+
+      <group choice=req>
+<!-- 	<arg rep=repeat><replaceable>seq1</replaceable></arg> -->
+<!-- 	<arg rep=repeat><replaceable>seq2</replaceable></arg> -->
+	<arg><replaceable> protein-input dna-input</replaceable></arg>
+      </group>
+
+    </cmdsynopsis>
+  </refsynopsisdiv>
+  <refsect1>
+    <title>DESCRIPTION</title>
+
+    <para>not available</para>
+
+  </refsect1>
+  <refsect1>
+    <title>OPTIONS</title>
+
+    <variablelist>
+      <varlistentry>
+        <term><option>-help</option>
+        </term>
+        <listitem>
+          <para>Show summary of options.</para>
+        </listitem>
+      </varlistentry>
+      <varlistentry>
+        <term><option>-version</option>
+        </term>
+        <listitem>
+          <para>Show version of program.</para>
+        </listitem>
+      </varlistentry>
+    </variablelist>
+  </refsect1>
+  <refsect1>
+    <title>SEE ALSO</title>
+
+    <para>dba (1), dnal (1), estwise (1), estwisedb (1), genewise (1), genomewise (1), promoterwise (1), psw (1), pswdb (1), scanwise (1), scanwise_server (1).</para>
+  </refsect1>
+  <refsect1>
+    <title>AUTHOR</title>
+
+    <para>This manual page was written by &dhusername; &dhemail; for
+      the &debian; system (but may be used by others).  Permission is
+      granted to copy, distribute and/or modify this document under
+      the terms of the &gnu; General Public License, Version 2 any 
+      later version published by the Free Software Foundation.
+    </para>
+    <para>
+      On Debian systems, the complete text of the GNU General Public
+      License can be found in /usr/share/common-licenses/GPL.
+    </para>
+
+  </refsect1>
+</refentry>
+
+<!-- Keep this comment at the end of the file
+Local variables:
+mode: sgml
+sgml-omittag:t
+sgml-shorttag:t
+sgml-minimize-attributes:nil
+sgml-always-quote-attributes:t
+sgml-indent-step:2
+sgml-indent-data:t
+sgml-parent-document:nil
+sgml-default-dtd-file:nil
+sgml-exposed-tags:nil
+sgml-local-catalogs:nil
+sgml-local-ecat-files:nil
+End:
+-->
+
+

Added: trunk/packages/wise/trunk/debian/manpages.d/genomewise.sgml
===================================================================
--- trunk/packages/wise/trunk/debian/manpages.d/genomewise.sgml	                        (rev 0)
+++ trunk/packages/wise/trunk/debian/manpages.d/genomewise.sgml	2007-09-17 07:14:21 UTC (rev 426)
@@ -0,0 +1,144 @@
+<!doctype refentry PUBLIC "-//OASIS//DTD DocBook V4.1//EN" [
+
+<!-- Process this file with docbook-to-man to generate an nroff manual
+     page: `docbook-to-man manpage.sgml > manpage.1'.  You may view
+     the manual page with: `docbook-to-man manpage.sgml | nroff -man |
+     less'.  A typical entry in a Makefile or Makefile.am is:
+
+manpage.1: manpage.sgml
+	docbook-to-man $< > $@
+
+    
+	The docbook-to-man binary is found in the docbook-to-man package.
+	Please remember that if you create the nroff version in one of the
+	debian/rules file targets (such as build), you will need to include
+	docbook-to-man in your Build-Depends control field.
+
+  -->
+
+
+  <!-- Fill in your name for FIRSTNAME and SURNAME. -->
+  <!ENTITY dhfirstname "<firstname>Philipp</firstname>">
+  <!ENTITY dhsurname   "<surname>Benner</surname>">
+  <!-- Please adjust the date whenever revising the manpage. -->
+  <!ENTITY dhdate      "<date>July 2006</date>">
+  <!-- SECTION should be 1-8, maybe w/ subsection other parameters are
+       allowed: see man(7), man(1). -->
+  <!ENTITY dhsection   "<manvolnum>1</manvolnum>">
+  <!ENTITY dhemail     "<email>mail at philipp-benner.de</email>">
+  <!ENTITY dhusername  "Philipp Benner">
+  <!ENTITY dhucpackage "<refentrytitle>GENOMEWISE</refentrytitle>">
+  <!ENTITY dhpackage   "genomewise">
+
+  <!ENTITY debian      "<productname>Debian</productname>">
+  <!ENTITY gnu         "<acronym>GNU</acronym>">
+  <!ENTITY gpl         "&gnu; <acronym>GPL</acronym>">
+]>
+
+<refentry>
+  <refentryinfo>
+    <address>
+      &dhemail;
+    </address>
+    <author>
+      &dhfirstname;
+      &dhsurname;
+    </author>
+    <copyright>
+      <year>2006</year>
+      <holder>&dhusername;</holder>
+    </copyright>
+    &dhdate;
+  </refentryinfo>
+  <refmeta>
+    &dhucpackage;
+
+    &dhsection;
+  </refmeta>
+  <refnamediv>
+    <refname>&dhpackage;</refname>
+
+    <refpurpose> </refpurpose>
+  </refnamediv>
+  <refsynopsisdiv>
+    <cmdsynopsis>
+      <command>&dhpackage;</command>
+
+      <group choice=opt>
+        <arg rep=repeat><replaceable>options</replaceable></arg>
+      </group>
+
+      <group choice=req>
+<!-- 	<arg rep=repeat><replaceable>seq1</replaceable></arg> -->
+<!-- 	<arg rep=repeat><replaceable>seq2</replaceable></arg> -->
+	<arg><replaceable> genomic-fasta-file evidence-file</replaceable></arg>
+      </group>
+
+    </cmdsynopsis>
+  </refsynopsisdiv>
+  <refsect1>
+    <title>DESCRIPTION</title>
+
+    <para>not available</para>
+
+  </refsect1>
+  <refsect1>
+    <title>OPTIONS</title>
+
+    <variablelist>
+      <varlistentry>
+        <term><option>-help</option>
+        </term>
+        <listitem>
+          <para>Show summary of options.</para>
+        </listitem>
+      </varlistentry>
+      <varlistentry>
+        <term><option>-version</option>
+        </term>
+        <listitem>
+          <para>Show version of program.</para>
+        </listitem>
+      </varlistentry>
+    </variablelist>
+  </refsect1>
+  <refsect1>
+    <title>SEE ALSO</title>
+
+    <para>dba (1), dnal (1), estwise (1), estwisedb (1), genewise (1), genewisedb (1), promoterwise (1), psw (1), pswdb (1), scanwise (1), scanwise_server (1).</para>
+  </refsect1>
+  <refsect1>
+    <title>AUTHOR</title>
+
+    <para>This manual page was written by &dhusername; &dhemail; for
+      the &debian; system (but may be used by others).  Permission is
+      granted to copy, distribute and/or modify this document under
+      the terms of the &gnu; General Public License, Version 2 any 
+      later version published by the Free Software Foundation.
+    </para>
+    <para>
+      On Debian systems, the complete text of the GNU General Public
+      License can be found in /usr/share/common-licenses/GPL.
+    </para>
+
+  </refsect1>
+</refentry>
+
+<!-- Keep this comment at the end of the file
+Local variables:
+mode: sgml
+sgml-omittag:t
+sgml-shorttag:t
+sgml-minimize-attributes:nil
+sgml-always-quote-attributes:t
+sgml-indent-step:2
+sgml-indent-data:t
+sgml-parent-document:nil
+sgml-default-dtd-file:nil
+sgml-exposed-tags:nil
+sgml-local-catalogs:nil
+sgml-local-ecat-files:nil
+End:
+-->
+
+

Added: trunk/packages/wise/trunk/debian/manpages.d/promoterwise.sgml
===================================================================
--- trunk/packages/wise/trunk/debian/manpages.d/promoterwise.sgml	                        (rev 0)
+++ trunk/packages/wise/trunk/debian/manpages.d/promoterwise.sgml	2007-09-17 07:14:21 UTC (rev 426)
@@ -0,0 +1,144 @@
+<!doctype refentry PUBLIC "-//OASIS//DTD DocBook V4.1//EN" [
+
+<!-- Process this file with docbook-to-man to generate an nroff manual
+     page: `docbook-to-man manpage.sgml > manpage.1'.  You may view
+     the manual page with: `docbook-to-man manpage.sgml | nroff -man |
+     less'.  A typical entry in a Makefile or Makefile.am is:
+
+manpage.1: manpage.sgml
+	docbook-to-man $< > $@
+
+    
+	The docbook-to-man binary is found in the docbook-to-man package.
+	Please remember that if you create the nroff version in one of the
+	debian/rules file targets (such as build), you will need to include
+	docbook-to-man in your Build-Depends control field.
+
+  -->
+
+
+  <!-- Fill in your name for FIRSTNAME and SURNAME. -->
+  <!ENTITY dhfirstname "<firstname>Philipp</firstname>">
+  <!ENTITY dhsurname   "<surname>Benner</surname>">
+  <!-- Please adjust the date whenever revising the manpage. -->
+  <!ENTITY dhdate      "<date>July 2006</date>">
+  <!-- SECTION should be 1-8, maybe w/ subsection other parameters are
+       allowed: see man(7), man(1). -->
+  <!ENTITY dhsection   "<manvolnum>1</manvolnum>">
+  <!ENTITY dhemail     "<email>mail at philipp-benner.de</email>">
+  <!ENTITY dhusername  "Philipp Benner">
+  <!ENTITY dhucpackage "<refentrytitle>PROMOTERWISE</refentrytitle>">
+  <!ENTITY dhpackage   "promoterwise">
+
+  <!ENTITY debian      "<productname>Debian</productname>">
+  <!ENTITY gnu         "<acronym>GNU</acronym>">
+  <!ENTITY gpl         "&gnu; <acronym>GPL</acronym>">
+]>
+
+<refentry>
+  <refentryinfo>
+    <address>
+      &dhemail;
+    </address>
+    <author>
+      &dhfirstname;
+      &dhsurname;
+    </author>
+    <copyright>
+      <year>2007</year>
+      <holder>&dhusername;</holder>
+    </copyright>
+    &dhdate;
+  </refentryinfo>
+  <refmeta>
+    &dhucpackage;
+
+    &dhsection;
+  </refmeta>
+  <refnamediv>
+    <refname>&dhpackage;</refname>
+
+    <refpurpose>comparison between two promoter sequences</refpurpose>
+  </refnamediv>
+  <refsynopsisdiv>
+    <cmdsynopsis>
+      <command>&dhpackage;</command>
+
+      <group choice=opt>
+        <arg rep=repeat><replaceable>options</replaceable></arg>
+      </group>
+
+      <group choice=req>
+<!-- 	<arg rep=repeat><replaceable>seq1</replaceable></arg> -->
+<!-- 	<arg rep=repeat><replaceable>seq2</replaceable></arg> -->
+	<arg><replaceable> query_sequence target_sequence</replaceable></arg>
+      </group>
+
+    </cmdsynopsis>
+  </refsynopsisdiv>
+  <refsect1>
+    <title>DESCRIPTION</title>
+
+    <para>not available</para>
+
+  </refsect1>
+  <refsect1>
+    <title>OPTIONS</title>
+
+    <variablelist>
+      <varlistentry>
+        <term><option>-help</option>
+        </term>
+        <listitem>
+          <para>Show summary of options.</para>
+        </listitem>
+      </varlistentry>
+      <varlistentry>
+        <term><option>-version</option>
+        </term>
+        <listitem>
+          <para>Show version of program.</para>
+        </listitem>
+      </varlistentry>
+    </variablelist>
+  </refsect1>
+  <refsect1>
+    <title>SEE ALSO</title>
+
+    <para>dba (1), dnal (1), estwise (1), estwisedb (1), genewisedb (1), genomewise (1), psw (1), pswdb (1) scanwise (1) scanwise_server (1).</para>
+  </refsect1>
+  <refsect1>
+    <title>AUTHOR</title>
+
+    <para>This manual page was written by &dhusername; &dhemail; for
+      the &debian; system (but may be used by others).  Permission is
+      granted to copy, distribute and/or modify this document under
+      the terms of the &gnu; General Public License, Version 2 any 
+      later version published by the Free Software Foundation.
+    </para>
+    <para>
+      On Debian systems, the complete text of the GNU General Public
+      License can be found in /usr/share/common-licenses/GPL.
+    </para>
+
+  </refsect1>
+</refentry>
+
+<!-- Keep this comment at the end of the file
+Local variables:
+mode: sgml
+sgml-omittag:t
+sgml-shorttag:t
+sgml-minimize-attributes:nil
+sgml-always-quote-attributes:t
+sgml-indent-step:2
+sgml-indent-data:t
+sgml-parent-document:nil
+sgml-default-dtd-file:nil
+sgml-exposed-tags:nil
+sgml-local-catalogs:nil
+sgml-local-ecat-files:nil
+End:
+-->
+
+

Added: trunk/packages/wise/trunk/debian/manpages.d/psw.sgml
===================================================================
--- trunk/packages/wise/trunk/debian/manpages.d/psw.sgml	                        (rev 0)
+++ trunk/packages/wise/trunk/debian/manpages.d/psw.sgml	2007-09-17 07:14:21 UTC (rev 426)
@@ -0,0 +1,149 @@
+<!doctype refentry PUBLIC "-//OASIS//DTD DocBook V4.1//EN" [
+
+<!-- Process this file with docbook-to-man to generate an nroff manual
+     page: `docbook-to-man manpage.sgml > manpage.1'.  You may view
+     the manual page with: `docbook-to-man manpage.sgml | nroff -man |
+     less'.  A typical entry in a Makefile or Makefile.am is:
+
+manpage.1: manpage.sgml
+	docbook-to-man $< > $@
+
+    
+	The docbook-to-man binary is found in the docbook-to-man package.
+	Please remember that if you create the nroff version in one of the
+	debian/rules file targets (such as build), you will need to include
+	docbook-to-man in your Build-Depends control field.
+
+  -->
+
+
+  <!-- Fill in your name for FIRSTNAME and SURNAME. -->
+  <!ENTITY dhfirstname "<firstname>Philipp</firstname>">
+  <!ENTITY dhsurname   "<surname>Benner</surname>">
+  <!-- Please adjust the date whenever revising the manpage. -->
+  <!ENTITY dhdate      "<date>July 2006</date>">
+  <!-- SECTION should be 1-8, maybe w/ subsection other parameters are
+       allowed: see man(7), man(1). -->
+  <!ENTITY dhsection   "<manvolnum>1</manvolnum>">
+  <!ENTITY dhemail     "<email>mail at philipp-benner.de</email>">
+  <!ENTITY dhusername  "Philipp Benner">
+  <!ENTITY dhucpackage "<refentrytitle>PSW</refentrytitle>">
+  <!ENTITY dhpackage   "psw">
+
+  <!ENTITY debian      "<productname>Debian</productname>">
+  <!ENTITY gnu         "<acronym>GNU</acronym>">
+  <!ENTITY gpl         "&gnu; <acronym>GPL</acronym>">
+]>
+
+<refentry>
+  <refentryinfo>
+    <address>
+      &dhemail;
+    </address>
+    <author>
+      &dhfirstname;
+      &dhsurname;
+    </author>
+    <copyright>
+      <year>2006</year>
+      <holder>&dhusername;</holder>
+    </copyright>
+    &dhdate;
+  </refentryinfo>
+  <refmeta>
+    &dhucpackage;
+
+    &dhsection;
+  </refmeta>
+  <refnamediv>
+    <refname>&dhpackage;</refname>
+
+    <refpurpose>Protein Smith-Waterman and other comparisons</refpurpose>
+  </refnamediv>
+  <refsynopsisdiv>
+    <cmdsynopsis>
+      <command>&dhpackage;</command>
+
+      <group choice=opt>
+        <arg rep=repeat><replaceable>options</replaceable></arg>
+      </group>
+
+      <group choice=req>
+<!-- 	<arg rep=repeat><replaceable>seq1</replaceable></arg> -->
+<!-- 	<arg rep=repeat><replaceable>seq2</replaceable></arg> -->
+	<arg><replaceable> seq1 seq2</replaceable></arg>
+      </group>
+
+    </cmdsynopsis>
+  </refsynopsisdiv>
+  <refsect1>
+    <title>DESCRIPTION</title>
+
+    <para>
+      psw is a short and sweet program for calculating smith waterman alginments
+      quickly. It was mainly written as C driver to test the underlying code which
+      is more useful in things like the Perl port.
+    </para>
+
+  </refsect1>
+
+  <refsect1>
+    <title>OPTIONS</title>
+
+    <variablelist>
+      <varlistentry>
+        <term><option>-help</option>
+        </term>
+        <listitem>
+          <para>Show summary of options.</para>
+        </listitem>
+      </varlistentry>
+      <varlistentry>
+        <term><option>-version</option>
+        </term>
+        <listitem>
+          <para>Show version of program.</para>
+        </listitem>
+      </varlistentry>
+    </variablelist>
+  </refsect1>
+  <refsect1>
+    <title>SEE ALSO</title>
+
+    <para>dba (1), dnal (1), estwise (1), estwisedb (1), genewise (1), genewisedb (1), genomewise (1), promoterwise (1), pswdb (1), scanwise (1), scanwise_server (1).</para>
+  </refsect1>
+  <refsect1>
+    <title>AUTHOR</title>
+
+    <para>This manual page was written by &dhusername; &dhemail; for
+      the &debian; system (but may be used by others).  Permission is
+      granted to copy, distribute and/or modify this document under
+      the terms of the &gnu; General Public License, Version 2 any 
+      later version published by the Free Software Foundation.
+    </para>
+    <para>
+      On Debian systems, the complete text of the GNU General Public
+      License can be found in /usr/share/common-licenses/GPL.
+    </para>
+
+  </refsect1>
+</refentry>
+
+<!-- Keep this comment at the end of the file
+Local variables:
+mode: sgml
+sgml-omittag:t
+sgml-shorttag:t
+sgml-minimize-attributes:nil
+sgml-always-quote-attributes:t
+sgml-indent-step:2
+sgml-indent-data:t
+sgml-parent-document:nil
+sgml-default-dtd-file:nil
+sgml-exposed-tags:nil
+sgml-local-catalogs:nil
+sgml-local-ecat-files:nil
+End:
+-->
+
+

Added: trunk/packages/wise/trunk/debian/manpages.d/pswdb.sgml
===================================================================
--- trunk/packages/wise/trunk/debian/manpages.d/pswdb.sgml	                        (rev 0)
+++ trunk/packages/wise/trunk/debian/manpages.d/pswdb.sgml	2007-09-17 07:14:21 UTC (rev 426)
@@ -0,0 +1,144 @@
+<!doctype refentry PUBLIC "-//OASIS//DTD DocBook V4.1//EN" [
+
+<!-- Process this file with docbook-to-man to generate an nroff manual
+     page: `docbook-to-man manpage.sgml > manpage.1'.  You may view
+     the manual page with: `docbook-to-man manpage.sgml | nroff -man |
+     less'.  A typical entry in a Makefile or Makefile.am is:
+
+manpage.1: manpage.sgml
+	docbook-to-man $< > $@
+
+    
+	The docbook-to-man binary is found in the docbook-to-man package.
+	Please remember that if you create the nroff version in one of the
+	debian/rules file targets (such as build), you will need to include
+	docbook-to-man in your Build-Depends control field.
+
+  -->
+
+
+  <!-- Fill in your name for FIRSTNAME and SURNAME. -->
+  <!ENTITY dhfirstname "<firstname>Philipp</firstname>">
+  <!ENTITY dhsurname   "<surname>Benner</surname>">
+  <!-- Please adjust the date whenever revising the manpage. -->
+  <!ENTITY dhdate      "<date>July 2006</date>">
+  <!-- SECTION should be 1-8, maybe w/ subsection other parameters are
+       allowed: see man(7), man(1). -->
+  <!ENTITY dhsection   "<manvolnum>1</manvolnum>">
+  <!ENTITY dhemail     "<email>mail at philipp-benner.de</email>">
+  <!ENTITY dhusername  "Philipp Benner">
+  <!ENTITY dhucpackage "<refentrytitle>PSWDB</refentrytitle>">
+  <!ENTITY dhpackage   "pswdb">
+
+  <!ENTITY debian      "<productname>Debian</productname>">
+  <!ENTITY gnu         "<acronym>GNU</acronym>">
+  <!ENTITY gpl         "&gnu; <acronym>GPL</acronym>">
+]>
+
+<refentry>
+  <refentryinfo>
+    <address>
+      &dhemail;
+    </address>
+    <author>
+      &dhfirstname;
+      &dhsurname;
+    </author>
+    <copyright>
+      <year>2006</year>
+      <holder>&dhusername;</holder>
+    </copyright>
+    &dhdate;
+  </refentryinfo>
+  <refmeta>
+    &dhucpackage;
+
+    &dhsection;
+  </refmeta>
+  <refnamediv>
+    <refname>&dhpackage;</refname>
+
+    <refpurpose>protein smith waterman database</refpurpose>
+  </refnamediv>
+  <refsynopsisdiv>
+    <cmdsynopsis>
+      <command>&dhpackage;</command>
+
+      <group choice=opt>
+        <arg rep=repeat><replaceable>options</replaceable></arg>
+      </group>
+
+      <group choice=req>
+<!-- 	<arg rep=repeat><replaceable>seq1</replaceable></arg> -->
+<!-- 	<arg rep=repeat><replaceable>seq2</replaceable></arg> -->
+	<arg><replaceable> query_db target_db</replaceable></arg>
+      </group>
+
+    </cmdsynopsis>
+  </refsynopsisdiv>
+  <refsect1>
+    <title>DESCRIPTION</title>
+
+    <para>not available</para>
+
+  </refsect1>
+  <refsect1>
+    <title>OPTIONS</title>
+
+    <variablelist>
+      <varlistentry>
+        <term><option>-help</option>
+        </term>
+        <listitem>
+          <para>Show summary of options.</para>
+        </listitem>
+      </varlistentry>
+      <varlistentry>
+        <term><option>-version</option>
+        </term>
+        <listitem>
+          <para>Show version of program.</para>
+        </listitem>
+      </varlistentry>
+    </variablelist>
+  </refsect1>
+  <refsect1>
+    <title>SEE ALSO</title>
+
+    <para>dba (1), dnal (1), estwise (1), estwisedb (1), genewise (1), genewisedb (1), genomewise (1), promoterwise (1), psw (1), scanwise (1), scanwise_server (1).</para>
+  </refsect1>
+  <refsect1>
+    <title>AUTHOR</title>
+
+    <para>This manual page was written by &dhusername; &dhemail; for
+      the &debian; system (but may be used by others).  Permission is
+      granted to copy, distribute and/or modify this document under
+      the terms of the &gnu; General Public License, Version 2 any 
+      later version published by the Free Software Foundation.
+    </para>
+    <para>
+      On Debian systems, the complete text of the GNU General Public
+      License can be found in /usr/share/common-licenses/GPL.
+    </para>
+
+  </refsect1>
+</refentry>
+
+<!-- Keep this comment at the end of the file
+Local variables:
+mode: sgml
+sgml-omittag:t
+sgml-shorttag:t
+sgml-minimize-attributes:nil
+sgml-always-quote-attributes:t
+sgml-indent-step:2
+sgml-indent-data:t
+sgml-parent-document:nil
+sgml-default-dtd-file:nil
+sgml-exposed-tags:nil
+sgml-local-catalogs:nil
+sgml-local-ecat-files:nil
+End:
+-->
+
+

Added: trunk/packages/wise/trunk/debian/manpages.d/scanwise.sgml
===================================================================
--- trunk/packages/wise/trunk/debian/manpages.d/scanwise.sgml	                        (rev 0)
+++ trunk/packages/wise/trunk/debian/manpages.d/scanwise.sgml	2007-09-17 07:14:21 UTC (rev 426)
@@ -0,0 +1,144 @@
+<!doctype refentry PUBLIC "-//OASIS//DTD DocBook V4.1//EN" [
+
+<!-- Process this file with docbook-to-man to generate an nroff manual
+     page: `docbook-to-man manpage.sgml > manpage.1'.  You may view
+     the manual page with: `docbook-to-man manpage.sgml | nroff -man |
+     less'.  A typical entry in a Makefile or Makefile.am is:
+
+manpage.1: manpage.sgml
+	docbook-to-man $< > $@
+
+    
+	The docbook-to-man binary is found in the docbook-to-man package.
+	Please remember that if you create the nroff version in one of the
+	debian/rules file targets (such as build), you will need to include
+	docbook-to-man in your Build-Depends control field.
+
+  -->
+
+
+  <!-- Fill in your name for FIRSTNAME and SURNAME. -->
+  <!ENTITY dhfirstname "<firstname>Philipp</firstname>">
+  <!ENTITY dhsurname   "<surname>Benner</surname>">
+  <!-- Please adjust the date whenever revising the manpage. -->
+  <!ENTITY dhdate      "<date>July 2006</date>">
+  <!-- SECTION should be 1-8, maybe w/ subsection other parameters are
+       allowed: see man(7), man(1). -->
+  <!ENTITY dhsection   "<manvolnum>1</manvolnum>">
+  <!ENTITY dhemail     "<email>mail at philipp-benner.de</email>">
+  <!ENTITY dhusername  "Philipp Benner">
+  <!ENTITY dhucpackage "<refentrytitle>SCANWISE</refentrytitle>">
+  <!ENTITY dhpackage   "scanwise">
+
+  <!ENTITY debian      "<productname>Debian</productname>">
+  <!ENTITY gnu         "<acronym>GNU</acronym>">
+  <!ENTITY gpl         "&gnu; <acronym>GPL</acronym>">
+]>
+
+<refentry>
+  <refentryinfo>
+    <address>
+      &dhemail;
+    </address>
+    <author>
+      &dhfirstname;
+      &dhsurname;
+    </author>
+    <copyright>
+      <year>2007</year>
+      <holder>&dhusername;</holder>
+    </copyright>
+    &dhdate;
+  </refentryinfo>
+  <refmeta>
+    &dhucpackage;
+
+    &dhsection;
+  </refmeta>
+  <refnamediv>
+    <refname>&dhpackage;</refname>
+
+    <refpurpose> </refpurpose>
+  </refnamediv>
+  <refsynopsisdiv>
+    <cmdsynopsis>
+      <command>&dhpackage;</command>
+
+      <group choice=opt>
+        <arg rep=repeat><replaceable>options</replaceable></arg>
+      </group>
+
+      <group choice=req>
+<!-- 	<arg rep=repeat><replaceable>seq1</replaceable></arg> -->
+<!-- 	<arg rep=repeat><replaceable>seq2</replaceable></arg> -->
+	<arg><replaceable> query_sequence_file_fasta</replaceable></arg>
+      </group>
+
+    </cmdsynopsis>
+  </refsynopsisdiv>
+  <refsect1>
+    <title>DESCRIPTION</title>
+
+    <para>not available</para>
+
+  </refsect1>
+  <refsect1>
+    <title>OPTIONS</title>
+
+    <variablelist>
+      <varlistentry>
+        <term><option>-help</option>
+        </term>
+        <listitem>
+          <para>Show summary of options.</para>
+        </listitem>
+      </varlistentry>
+      <varlistentry>
+        <term><option>-version</option>
+        </term>
+        <listitem>
+          <para>Show version of program.</para>
+        </listitem>
+      </varlistentry>
+    </variablelist>
+  </refsect1>
+  <refsect1>
+    <title>SEE ALSO</title>
+
+    <para>dba (1), dnal (1), estwise (1), estwisedb (1), genewisedb (1), genomewise (1), promoterwise (1), psw (1), pswdb (1), scanwise_server (1).</para>
+  </refsect1>
+  <refsect1>
+    <title>AUTHOR</title>
+
+    <para>This manual page was written by &dhusername; &dhemail; for
+      the &debian; system (but may be used by others).  Permission is
+      granted to copy, distribute and/or modify this document under
+      the terms of the &gnu; General Public License, Version 2 any 
+      later version published by the Free Software Foundation.
+    </para>
+    <para>
+      On Debian systems, the complete text of the GNU General Public
+      License can be found in /usr/share/common-licenses/GPL.
+    </para>
+
+  </refsect1>
+</refentry>
+
+<!-- Keep this comment at the end of the file
+Local variables:
+mode: sgml
+sgml-omittag:t
+sgml-shorttag:t
+sgml-minimize-attributes:nil
+sgml-always-quote-attributes:t
+sgml-indent-step:2
+sgml-indent-data:t
+sgml-parent-document:nil
+sgml-default-dtd-file:nil
+sgml-exposed-tags:nil
+sgml-local-catalogs:nil
+sgml-local-ecat-files:nil
+End:
+-->
+
+

Added: trunk/packages/wise/trunk/debian/manpages.d/scanwise_server.sgml
===================================================================
--- trunk/packages/wise/trunk/debian/manpages.d/scanwise_server.sgml	                        (rev 0)
+++ trunk/packages/wise/trunk/debian/manpages.d/scanwise_server.sgml	2007-09-17 07:14:21 UTC (rev 426)
@@ -0,0 +1,144 @@
+<!doctype refentry PUBLIC "-//OASIS//DTD DocBook V4.1//EN" [
+
+<!-- Process this file with docbook-to-man to generate an nroff manual
+     page: `docbook-to-man manpage.sgml > manpage.1'.  You may view
+     the manual page with: `docbook-to-man manpage.sgml | nroff -man |
+     less'.  A typical entry in a Makefile or Makefile.am is:
+
+manpage.1: manpage.sgml
+	docbook-to-man $< > $@
+
+    
+	The docbook-to-man binary is found in the docbook-to-man package.
+	Please remember that if you create the nroff version in one of the
+	debian/rules file targets (such as build), you will need to include
+	docbook-to-man in your Build-Depends control field.
+
+  -->
+
+
+  <!-- Fill in your name for FIRSTNAME and SURNAME. -->
+  <!ENTITY dhfirstname "<firstname>Philipp</firstname>">
+  <!ENTITY dhsurname   "<surname>Benner</surname>">
+  <!-- Please adjust the date whenever revising the manpage. -->
+  <!ENTITY dhdate      "<date>July 2006</date>">
+  <!-- SECTION should be 1-8, maybe w/ subsection other parameters are
+       allowed: see man(7), man(1). -->
+  <!ENTITY dhsection   "<manvolnum>1</manvolnum>">
+  <!ENTITY dhemail     "<email>mail at philipp-benner.de</email>">
+  <!ENTITY dhusername  "Philipp Benner">
+  <!ENTITY dhucpackage "<refentrytitle>SCANWISE_SERVER</refentrytitle>">
+  <!ENTITY dhpackage   "scanwise_server">
+
+  <!ENTITY debian      "<productname>Debian</productname>">
+  <!ENTITY gnu         "<acronym>GNU</acronym>">
+  <!ENTITY gpl         "&gnu; <acronym>GPL</acronym>">
+]>
+
+<refentry>
+  <refentryinfo>
+    <address>
+      &dhemail;
+    </address>
+    <author>
+      &dhfirstname;
+      &dhsurname;
+    </author>
+    <copyright>
+      <year>2006</year>
+      <holder>&dhusername;</holder>
+    </copyright>
+    &dhdate;
+  </refentryinfo>
+  <refmeta>
+    &dhucpackage;
+
+    &dhsection;
+  </refmeta>
+  <refnamediv>
+    <refname>&dhpackage;</refname>
+
+    <refpurpose> </refpurpose>
+  </refnamediv>
+  <refsynopsisdiv>
+    <cmdsynopsis>
+      <command>&dhpackage;</command>
+
+      <group choice=opt>
+        <arg rep=repeat><replaceable>options</replaceable></arg>
+      </group>
+
+      <group choice=req>
+<!-- 	<arg rep=repeat><replaceable>seq1</replaceable></arg> -->
+<!-- 	<arg rep=repeat><replaceable>seq2</replaceable></arg> -->
+	<arg><replaceable> sequence_file_fasta</replaceable></arg>
+      </group>
+
+    </cmdsynopsis>
+  </refsynopsisdiv>
+  <refsect1>
+    <title>DESCRIPTION</title>
+
+    <para>not available</para>
+
+  </refsect1>
+  <refsect1>
+    <title>OPTIONS</title>
+
+    <variablelist>
+      <varlistentry>
+        <term><option>-help</option>
+        </term>
+        <listitem>
+          <para>Show summary of options.</para>
+        </listitem>
+      </varlistentry>
+      <varlistentry>
+        <term><option>-version</option>
+        </term>
+        <listitem>
+          <para>Show version of program.</para>
+        </listitem>
+      </varlistentry>
+    </variablelist>
+  </refsect1>
+  <refsect1>
+    <title>SEE ALSO</title>
+
+    <para>dba (1), dnal (1), estwise (1), estwisedb (1), genewisedb (1), genomewise (1), promoterwise (1), psw (1), pswdb (1), scanwise (1), scanwise_server (1).</para>
+  </refsect1>
+  <refsect1>
+    <title>AUTHOR</title>
+
+    <para>This manual page was written by &dhusername; &dhemail; for
+      the &debian; system (but may be used by others).  Permission is
+      granted to copy, distribute and/or modify this document under
+      the terms of the &gnu; General Public License, Version 2 any 
+      later version published by the Free Software Foundation.
+    </para>
+    <para>
+      On Debian systems, the complete text of the GNU General Public
+      License can be found in /usr/share/common-licenses/GPL.
+    </para>
+
+  </refsect1>
+</refentry>
+
+<!-- Keep this comment at the end of the file
+Local variables:
+mode: sgml
+sgml-omittag:t
+sgml-shorttag:t
+sgml-minimize-attributes:nil
+sgml-always-quote-attributes:t
+sgml-indent-step:2
+sgml-indent-data:t
+sgml-parent-document:nil
+sgml-default-dtd-file:nil
+sgml-exposed-tags:nil
+sgml-local-catalogs:nil
+sgml-local-ecat-files:nil
+End:
+-->
+
+

Added: trunk/packages/wise/trunk/debian/patches/00list
===================================================================
--- trunk/packages/wise/trunk/debian/patches/00list	                        (rev 0)
+++ trunk/packages/wise/trunk/debian/patches/00list	2007-09-17 07:14:21 UTC (rev 426)
@@ -0,0 +1,4 @@
+01_welcome-csh
+02_isnumber
+03_doc-nodycache
+04_wise2-pdflatex-update

Added: trunk/packages/wise/trunk/debian/patches/01_welcome-csh.dpatch
===================================================================
--- trunk/packages/wise/trunk/debian/patches/01_welcome-csh.dpatch	                        (rev 0)
+++ trunk/packages/wise/trunk/debian/patches/01_welcome-csh.dpatch	2007-09-17 07:14:21 UTC (rev 426)
@@ -0,0 +1,28 @@
+#! /bin/sh /usr/share/dpatch/dpatch-run
+## 01_welcome-csh.dpatch by Philipp Benner <mail at philipp-benner.de>
+##
+## All lines beginning with `## DP:' are a description of the patch.
+## DP: No description.
+
+ at DPATCH@
+diff -urNad wise-2.4.0~/src/makefile wise-2.4.0/src/makefile
+--- wise-2.4.0~/src/makefile	2007-07-15 23:39:24.000000000 +0200
++++ wise-2.4.0/src/makefile	2007-07-15 23:41:11.000000000 +0200
+@@ -109,7 +109,7 @@
+ bin : 
+ 	mkdir bin
+ 	cp models/pswdb models/psw models/genewisedb models/estwisedb models/estwise models/genewise models/dba models/dnal models/promoterwise network/scanwise_server models/scanwise ./bin
+-	csh welcome.csh
++	./welcome.csh
+ 
+ libs : 
+ 	(cd base   ; $(MAKE) CC="$(CC)" CFLAGS="$(CFLAGS)" libwisebase.a )
+diff -urNad wise-2.4.0~/src/welcome.csh wise-2.4.0/src/welcome.csh
+--- wise-2.4.0~/src/welcome.csh	2007-07-15 23:39:24.000000000 +0200
++++ wise-2.4.0/src/welcome.csh	2007-07-15 23:40:46.000000000 +0200
+@@ -1,4 +1,4 @@
+-#!/bin/tcsh -f
++#!/bin/sh
+ 
+ echo ""
+ echo "Welcome to Wise2.4"


Property changes on: trunk/packages/wise/trunk/debian/patches/01_welcome-csh.dpatch
___________________________________________________________________
Name: svn:executable
   + *

Added: trunk/packages/wise/trunk/debian/patches/02_isnumber.dpatch
===================================================================
--- trunk/packages/wise/trunk/debian/patches/02_isnumber.dpatch	                        (rev 0)
+++ trunk/packages/wise/trunk/debian/patches/02_isnumber.dpatch	2007-09-17 07:14:21 UTC (rev 426)
@@ -0,0 +1,18 @@
+#! /bin/sh /usr/share/dpatch/dpatch-run
+## 02_isnumber.dpatch by Philipp Benner <mail at philipp-benner.de>
+##
+## DP: Replace isnumber() (which does not exist on linux) by isdigit().
+
+ at DPATCH@
+diff -urNad wise-2.4.0~/src/models/phasemodel.c wise-2.4.0/src/models/phasemodel.c
+--- wise-2.4.0~/src/models/phasemodel.c	2007-07-01 22:44:39.000000000 +0200
++++ wise-2.4.0/src/models/phasemodel.c	2007-07-16 00:24:16.000000000 +0200
+@@ -20,7 +20,7 @@
+     if( line[0] == '#' ) {
+       continue;
+     }
+-    if( !isnumber(line[0]) ) {
++    if( !isdigit(line[0]) ) {
+       warn("Bad looking line in intron file, %s",line);
+       continue;
+     }


Property changes on: trunk/packages/wise/trunk/debian/patches/02_isnumber.dpatch
___________________________________________________________________
Name: svn:executable
   + *

Added: trunk/packages/wise/trunk/debian/patches/03_doc-nodycache.dpatch
===================================================================
--- trunk/packages/wise/trunk/debian/patches/03_doc-nodycache.dpatch	                        (rev 0)
+++ trunk/packages/wise/trunk/debian/patches/03_doc-nodycache.dpatch	2007-09-17 07:14:21 UTC (rev 426)
@@ -0,0 +1,19 @@
+#! /bin/sh /usr/share/dpatch/dpatch-run
+## 03_doc-nodycache.dpatch by Philipp Benner <mail at philipp-benner.de>
+##
+## DP: Documentation bugfix.
+
+ at DPATCH@
+diff -urNad wise-2.4.0~/docs/wise2.tex wise-2.4.0/docs/wise2.tex
+--- wise-2.4.0~/docs/wise2.tex	2003-03-26 12:47:08.000000000 +0100
++++ wise-2.4.0/docs/wise2.tex	2007-07-16 01:05:34.000000000 +0200
+@@ -1617,7 +1617,8 @@
+ \item[-hithelp]   more detailed help on hitlist formats
+ \item[-dymem]      memory style [default/linear/explicit]
+ \item[-kbyte]       memory amount to use [4000]
+-\item[-\[no\]dycache] implicitly cache dy matrix usage (default yes)
++\item[-dycache] implicitly cache dy matrix usage (default)
++\item[-nodycache] do not implicitly cache dy matrix usage
+ \item[-dydebug]     drop into dynamite dp matrix debugger
+ \item[-paldebug]    print PackAln after debugger run if used
+ \item[-help]      show help options


Property changes on: trunk/packages/wise/trunk/debian/patches/03_doc-nodycache.dpatch
___________________________________________________________________
Name: svn:executable
   + *

Added: trunk/packages/wise/trunk/debian/patches/04_wise2-pdflatex-update.dpatch
===================================================================
--- trunk/packages/wise/trunk/debian/patches/04_wise2-pdflatex-update.dpatch	                        (rev 0)
+++ trunk/packages/wise/trunk/debian/patches/04_wise2-pdflatex-update.dpatch	2007-09-17 07:14:21 UTC (rev 426)
@@ -0,0 +1,43 @@
+#! /bin/sh /usr/share/dpatch/dpatch-run
+## 04_wise2-pdflatex-update.dpatch by Philipp Benner <mail at philipp-benner.de>
+##
+## DP: Make wise2.tex pdflatex compatible.
+
+ at DPATCH@
+
+diff -urNad wise-2.4.0~/docs/wise2.tex wise-2.4.0/docs/wise2.tex
+--- wise-2.4.0~/docs/wise2.tex	2007-08-06 10:25:05.000000000 +0200
++++ wise-2.4.0/docs/wise2.tex	2007-08-06 10:25:08.000000000 +0200
+@@ -1,6 +1,7 @@
+ 
+ \documentclass{article}
+-\usepackage{epsfig}
++%\usepackage{epsfig}
++\usepackage{graphicx}
+ 
+ \begin{document}
+ \newcommand{\programtext}[1]{{\tt #1}}
+@@ -707,8 +708,9 @@
+ \begin{figure}
+ \begin{center}
+ \leavevmode  
+-\epsfxsize 300pt
+-\epsfbox{genewise21.eps}
++%\epsfxsize 300pt
++%\epsfbox{genewise21.eps}
++%\includegraphics[scale=0.75]{genewise21.pdf}
+ \newline     
+ \caption{GeneWise21:93 Algorithm. The dark circles represent states, and the
+ arrows between them transitions. Black transitions are standard
+@@ -898,8 +900,9 @@
+ \begin{figure}
+ \begin{center}
+ \leavevmode  
+-\epsfxsize 300pt
+-\epsfbox{genewise6.eps}
++%\epsfxsize 300pt
++%\epsfbox{genewise6.eps}
++%\includegraphics[scale=0.75]{genewise6.pdf}
+ \newline     
+ \caption{GeneWise6:23}
+ \label{Figure:genewise623}


Property changes on: trunk/packages/wise/trunk/debian/patches/04_wise2-pdflatex-update.dpatch
___________________________________________________________________
Name: svn:executable
   + *

Added: trunk/packages/wise/trunk/debian/rules
===================================================================
--- trunk/packages/wise/trunk/debian/rules	                        (rev 0)
+++ trunk/packages/wise/trunk/debian/rules	2007-09-17 07:14:21 UTC (rev 426)
@@ -0,0 +1,151 @@
+#!/usr/bin/make -f
+# -*- makefile -*-
+
+# Uncomment this to turn on verbose mode.
+#export DH_VERBOSE=1
+
+CFLAGS = -Wall -g
+
+ifneq (,$(findstring noopt,$(DEB_BUILD_OPTIONS)))
+	CFLAGS += -O0
+else
+	CFLAGS += -O2
+endif
+
+.NOTPARALLEL:
+include /usr/share/dpatch/dpatch.make
+
+configure: configure-stamp
+configure-stamp:
+	dh_testdir
+
+	touch configure-stamp
+
+build: patch build-stamp
+
+build-stamp: configure-stamp 
+	dh_testdir
+
+	$(MAKE) -C src all
+	$(MAKE) -C debian/manpages.d
+
+#	build documentation manually (docs/makefile is not useable)
+	cat src/models/*.tex src/dynlibsrc/*.tex | perl docs/gettex.pl > docs/temp.tex
+	cat docs/wise2api.tex docs/temp.tex docs/apiend.tex > docs/api.tex
+#	<bugfix>
+	sed -i 's/ sw_wrap / sw\\_wrap /' docs/api.tex
+	sed -i 's/label{module_sequence\\_codon}/label{module_sequence_codon}/' docs/api.tex
+	sed -i 's/Wise2::GeneParameter21_wrap/Wise2::GeneParameter21\\_wrap/' docs/api.tex
+#	</bugfix>
+	cd docs && pdflatex api.tex
+	cd docs && pdflatex api.tex
+	cd docs && pdflatex dynamite.tex
+	cd docs && pdflatex dynamite.tex
+#	cd docs && ps2pdf genewise6.eps  # segfaults on s390
+#	cd docs && ps2pdf genewise21.eps
+	cd docs && pdflatex wise2.tex
+	cd docs && pdflatex wise2.tex
+
+	cd docs && hevea api.tex
+	cd docs && hevea api.tex
+	cd docs && hevea dynamite.tex
+	cd docs && hevea dynamite.tex
+	cd docs && hevea wise2.tex
+	cd docs && hevea wise2.tex
+
+	mkdir -p docs/api
+	mkdir -p docs/dynamite
+	mkdir -p docs/wise2
+
+	mv docs/api.html docs/api
+	mv docs/dynamite.html docs/dynamite
+	mv docs/wise2.html docs/wise2
+
+	touch $@
+
+clean: unpatch
+	dh_testdir
+	dh_testroot
+	rm -f build-stamp configure-stamp
+
+	$(MAKE) -C src clean
+	$(MAKE) -C debian/manpages.d clean
+
+#	bugfix
+	$(RM) -r src/oldbin
+	$(RM) src/models/{dba,psw,dnal,genomewise,pswdb,scanwise,estwise,genewise,sywise,genewisedb,promoterwise,pseudowise,estwisedb}
+	$(RM) src/network/scanwise_server
+
+#	clean documentation
+	$(RM) docs/temp.tex
+	$(RM) docs/api.*
+	$(RM) docs/wise2.image.tex
+	$(RM) docs/*.pdf
+	$(RM) docs/*.aux
+	$(RM) docs/*.log
+	$(RM) docs/*.toc
+	$(RM) docs/*.pdf
+	$(RM) docs/*.dvi
+	$(RM) docs/*.ps
+	$(RM) docs/*.4ct
+	$(RM) docs/*.4tc
+	$(RM) docs/*.css
+	$(RM) docs/*.idv
+	$(RM) docs/*.lg
+	$(RM) docs/*.tmp
+	$(RM) docs/*.xref
+	$(RM) docs/*.haux
+	$(RM) docs/*.htoc
+	$(RM) docs/*.html
+
+	$(RM) -r docs/api
+	$(RM) -r docs/dynamite
+	$(RM) -r docs/wise2
+
+	dh_clean
+
+install: build
+	dh_testdir
+	dh_testroot
+	dh_clean -k 
+	dh_installdirs
+
+#	$(MAKE) install DESTDIR=$(CURDIR)/debian/wise
+	install -m 755 src/bin/* debian/wise/usr/bin
+	install -m 755 src/models/genomewise debian/wise/usr/bin
+
+binary-indep: build install
+	dh_testdir -i
+	dh_testroot -i
+	dh_installchangelogs -i
+	dh_installdocs -i
+	dh_installexamples -i
+	dh_installman -i
+	dh_link -i
+	dh_strip -i
+	dh_compress -i
+	dh_fixperms -i
+	dh_installdeb -i
+	dh_gencontrol -i
+	dh_md5sums -i
+	dh_builddeb -i
+
+binary-arch: build install
+	dh_testdir -a
+	dh_testroot -a
+	dh_installchangelogs -a
+	dh_installdocs -a
+	dh_installexamples -a
+	dh_installman -a
+	dh_link -a
+	dh_strip -a
+	dh_compress -a
+	dh_fixperms -a
+	dh_installdeb -a
+	dh_shlibdeps -a
+	dh_gencontrol -a
+	dh_md5sums -a
+	dh_builddeb -a
+
+binary: binary-indep binary-arch
+.PHONY: build clean binary-indep binary-arch binary install configure


Property changes on: trunk/packages/wise/trunk/debian/rules
___________________________________________________________________
Name: svn:executable
   + *

Added: trunk/packages/wise/trunk/debian/watch
===================================================================
--- trunk/packages/wise/trunk/debian/watch	                        (rev 0)
+++ trunk/packages/wise/trunk/debian/watch	2007-09-17 07:14:21 UTC (rev 426)
@@ -0,0 +1,9 @@
+# Compulsory line, this is a version 3 file
+version=3
+
+# official wise2 ftp site
+#ftp://ftp.ebi.ac.uk/pub/software/unix/wise2/wise(.*)\.tar\.gz \
+#	debian uupdate
+
+http://www.ebi.ac.uk/~birney/wise2/ (?:./)?wise(.*)\.tar\.gz \
+  debian uupdate

Added: trunk/packages/wise/trunk/debian/wise-doc.doc-base.api
===================================================================
--- trunk/packages/wise/trunk/debian/wise-doc.doc-base.api	                        (rev 0)
+++ trunk/packages/wise/trunk/debian/wise-doc.doc-base.api	2007-09-17 07:14:21 UTC (rev 426)
@@ -0,0 +1,12 @@
+Document: wise-api
+Title: Debian wise api Manual
+Author: Ewan Birney
+Abstract: This manual describes the wise api.
+Section: science
+
+Format: PDF
+Files: /usr/share/doc/wise-doc/api.pdf.gz
+
+Format: HTML
+Index: /usr/share/doc/wise-doc/api/api.html
+Files: /usr/share/doc/wise-doc/api/*

Added: trunk/packages/wise/trunk/debian/wise-doc.doc-base.dynamite
===================================================================
--- trunk/packages/wise/trunk/debian/wise-doc.doc-base.dynamite	                        (rev 0)
+++ trunk/packages/wise/trunk/debian/wise-doc.doc-base.dynamite	2007-09-17 07:14:21 UTC (rev 426)
@@ -0,0 +1,13 @@
+Document: wise-dynamite
+Title: Debian wise dynamite Manual
+Author: Ewan Birney
+Abstract: This manual describes the dynamite code generating
+ language for dynamic programming.
+Section: science
+
+Format: PDF
+Files: /usr/share/doc/wise-doc/dynamite.pdf.gz
+
+Format: HTML
+Index: /usr/share/doc/wise-doc/dynamite/dynamite.html
+Files: /usr/share/doc/wise-doc/dynamite/*

Added: trunk/packages/wise/trunk/debian/wise-doc.doc-base.wise
===================================================================
--- trunk/packages/wise/trunk/debian/wise-doc.doc-base.wise	                        (rev 0)
+++ trunk/packages/wise/trunk/debian/wise-doc.doc-base.wise	2007-09-17 07:14:21 UTC (rev 426)
@@ -0,0 +1,12 @@
+Document: wise
+Title: Debian wise2 Manual
+Author: Ewan Birney, Richard Copley
+Abstract: This manual describes wise program usages.
+Section: science
+
+Format: PDF
+Files: /usr/share/doc/wise-doc/wise2.pdf.gz
+
+Format: HTML
+Index: /usr/share/doc/wise-doc/wise2/wise2.html
+Files: /usr/share/doc/wise-doc/wise2/*

Added: trunk/packages/wise/trunk/debian/wise-doc.docs
===================================================================
--- trunk/packages/wise/trunk/debian/wise-doc.docs	                        (rev 0)
+++ trunk/packages/wise/trunk/debian/wise-doc.docs	2007-09-17 07:14:21 UTC (rev 426)
@@ -0,0 +1,6 @@
+docs/api.pdf
+docs/dynamite.pdf
+docs/wise2.pdf
+docs/api
+docs/dynamite
+docs/wise2

Added: trunk/packages/wise/trunk/debian/wise-doc.examples
===================================================================
--- trunk/packages/wise/trunk/debian/wise-doc.examples	                        (rev 0)
+++ trunk/packages/wise/trunk/debian/wise-doc.examples	2007-09-17 07:14:21 UTC (rev 426)
@@ -0,0 +1 @@
+wisecfg/*




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