primer3 (1.1.4-1) debian-dir only changes

Summary

 debian/README.Debian      |    9 +
 debian/changelog          |   84 +++++++++++++++++
 debian/control            |   33 ++++++
 debian/copyright          |   67 +++++++++++++
 debian/ntdpal.1           |  112 +++++++++++++++++++++++
 debian/ntdpal.1.xml       |  222 ++++++++++++++++++++++++++++++++++++++++++++++
 debian/oligotm.1          |  114 +++++++++++++++++++++++
 debian/oligotm.1.xml      |  189 +++++++++++++++++++++++++++++++++++++++
 debian/primer3.docs       |    3 
 debian/primer3.examples   |    1 
 debian/primer3.install    |    4 
 debian/primer3.manpages   |    3 
 debian/primer3_core.1     |   90 ++++++++++++++++++
 debian/primer3_core.1.xml |  153 +++++++++++++++++++++++++++++++
 debian/rules              |   11 ++
 debian/watch              |    2 
 16 files changed, 1097 insertions(+)

    
download this patch

Patch contents

--- primer3-1.1.4.orig/debian/watch
+++ primer3-1.1.4/debian/watch
@@ -0,0 +1,2 @@
+version=3
+http://sf.net/primer3/primer3-([\d.]*)\.tar\.gz
--- primer3-1.1.4.orig/debian/oligotm.1.xml
+++ primer3-1.1.4/debian/oligotm.1.xml
@@ -0,0 +1,189 @@
+<?xml version='1.0' encoding='UTF-8'?>
+<?xml-stylesheet type="text/xsl"
+        href="http://docbook.sourceforge.net/release/xsl/current/manpages/docbook.xsl"?>
+<!DOCTYPE refentry PUBLIC "-//OASIS//DTD DocBook XML V4.5//EN"
+        "http://www.oasis-open.org/docbook/xml/4.5/docbookx.dtd" [
+  <!ENTITY dhfirstname "<firstname>Charles</firstname>">
+  <!ENTITY dhsurname   "<surname>Plessy</surname>">
+  <!ENTITY dhsection   "<manvolnum>1</manvolnum>">
+  <!ENTITY dhemail     "<email>plessy@debian.org</email>">
+  <!ENTITY dhusername  "Charles Plessy">
+  <!ENTITY dhucpackage "<refentrytitle>OLIGOTM</refentrytitle>">
+  <!ENTITY dhtitle     "Primer3 User Manuals">
+  <!ENTITY dhpackage   "oligotm">
+  <!ENTITY dhrelease   "1.1.4">
+  <!ENTITY debian      "<productname>Debian</productname>">
+  <!ENTITY gnu         "<acronym>GNU</acronym>">
+  <!ENTITY gpl         "&gnu; <acronym>GPL</acronym>">
+]>
+
+<refentry>
+  <refentryinfo>
+    <title>&dhtitle;</title>
+    <productname>&dhpackage;</productname>
+    <releaseinfo role="version">&dhrelease;</releaseinfo>
+    <address>
+      &dhemail;
+    </address>
+  <!--   <author>
+      &dhfirstname;
+      &dhsurname;
+    </author> -->
+    <copyright>
+      <year>1996,1997,1998,1999,2000,2001,2004,2006,2007,2008</year>
+      <holder>Whitehead Institute for Biomedical Research</holder>
+      <holder>Steve Rozen (http://jura.wi.mit.edu/rozen)</holder>
+      <holder>Helen Skaletsky</holder>
+    </copyright>
+    
+    <legalnotice>
+      <para>All rights reserved. On Debian-based systems, please consult <filename>/usr/share/doc/primer3/copyright</filename> to read the licence of &dhpackage;.</para>
+    </legalnotice>
+    
+    <legalnotice>
+      <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 same terms as oligotm itself.<!-- This also applies to this source document --></para>
+    </legalnotice>
+  </refentryinfo>
+
+  <refmeta>
+    &dhucpackage;
+    &dhsection;
+  </refmeta>
+  
+  <refnamediv>
+    <refname>&dhpackage;</refname>
+    <refpurpose>Prints oligo's melting temperature on stdout</refpurpose>
+  </refnamediv>
+  
+  <refsynopsisdiv>
+    <cmdsynopsis>
+      <command>&dhpackage;</command>
+        <arg choice="opt">OPTIONS</arg>
+        <arg choice="req">oligo</arg>
+    </cmdsynopsis>
+    <para>where oligo is a DNA sequence of between 2 and 36 bases</para>
+  </refsynopsisdiv>
+  
+  <refsect1  id="description">
+    <title>DESCRIPTION</title>
+    <para>
+      <command>&dhpackage;</command> prints the melting temperature of a given desoxyribooligonucleotide on the standard output. It is part of the oligotm library.
+    </para>
+  </refsect1>
+  
+  <refsect1 id="options">
+    <title>OPTIONS</title>
+    <variablelist>
+      <varlistentry>
+        <term>
+          <option>-mv</option> <parameter>monovalent_conc</parameter>
+        </term>
+        <listitem>
+          <para>Concentration of monovalent cations in mM, by default 50&nbsp;mM.</para>
+        </listitem>
+      </varlistentry>
+
+      <varlistentry>
+        <term>
+          <option>-dv</option> <parameter>divalent_conc</parameter>
+        </term>
+        <listitem>
+          <para>Concentration of divalent cations in mM, by default 0&nbsp;mM.</para>
+        </listitem>
+      </varlistentry>
+
+      <varlistentry>
+        <term>
+          <option>-n</option> <parameter>dNTP_conc</parameter>
+        </term>
+        <listitem>
+          <para>Concentration of deoxynycleotide triphosphate in mM, by default 0&nbsp;mM.</para>
+        </listitem>
+      </varlistentry>
+      
+      <varlistentry>
+        <term>
+          <option>-d</option> <parameter>dna_conc</parameter>
+        </term>
+        <listitem>
+          <para>Concentration of DNA strands in nM, by default 50&nbsp;nM.</para>
+        </listitem>
+      </varlistentry>
+
+      <varlistentry>
+        <term>
+          <option>-tp</option> <parameter>[0|1]</parameter>
+        </term>
+        <listitem>
+          <para>Specifies the table of thermodynamic parameters and
+                the method of melting temperature calculation:</para>
+          <itemizedlist>
+            <listitem>
+              <para><parameter>0</parameter> Breslauer et al., 1986 and Rychlik et al., 1990 (used by primer3 up to and including release 1.1.0). This is the default, but <emphasis>not</emphasis> the recommended value.</para>
+            </listitem>
+            <listitem>
+              <para><parameter>1</parameter> Use nearest neighbor parameter from SantaLucia 1998. <emphasis>This is the recommended value</emphasis>.</para>
+            </listitem>
+          </itemizedlist>
+        </listitem>
+      </varlistentry>
+      
+      <varlistentry>
+        <term>
+          <option>-sc</option> <parameter>[0..2]</parameter>
+        </term>
+        <listitem>
+          <para>Specifies salt correction formula for the melting temperature calculation:</para>
+          <itemizedlist>
+            <listitem>
+              <para><parameter>0</parameter> Schildkraut and Lifson 1965, used by primer3 up to and including release 1.1.0. This is the default, but <emphasis>not</emphasis> the recommended value.</para>
+            </listitem>
+            <listitem>
+              <para><parameter>1</parameter> SantaLucia 1998. <emphasis>This is the recommended value</emphasis>.</para>
+            </listitem>
+             <listitem>
+              <para><parameter>1</parameter> Owczarzy et al., 2004.</para>
+            </listitem>
+          </itemizedlist>
+        </listitem>
+      </varlistentry>
+            
+      <varlistentry>
+        <term>
+          <option>-i</option>
+        </term>
+        <listitem>
+          <para>prints references to publications which were used for thermodynamic calculations.</para>
+        </listitem>
+      </varlistentry>
+     </variablelist>
+  </refsect1>
+
+  <refsect1 id="reference">
+    <title>REFERENCE</title>
+    <para>
+    Please cite Rozen, S., Skaletsky, H.  "Primer3 on the WWW for general users
+    and for biologist programmers."  In S. Krawetz and
+   S. Misener, eds. Bioinformatics Methods and Protocols in
+   the series Methods in Molecular Biology.  Humana Press,
+   Totowa, NJ, 2000, pages 365-386.
+    </para> 
+  </refsect1>
+  
+  <refsect1 id="see_also">
+    <title>SEE ALSO</title>
+    <para>
+      <citerefentry>
+        <refentrytitle>primer3_core</refentrytitle>
+        <manvolnum>1</manvolnum>
+      </citerefentry>
+      <citerefentry>
+        <refentrytitle>ntdpal</refentrytitle>
+        <manvolnum>1</manvolnum>
+      </citerefentry>
+    </para>
+  </refsect1>
+</refentry>
--- primer3-1.1.4.orig/debian/primer3.install
+++ primer3-1.1.4/debian/primer3.install
@@ -0,0 +1,4 @@
+src/primer3_core	usr/bin
+src/ntdpal		usr/bin
+src/oligotm		usr/bin
+#src/long_seq_tm_test	usr/bin
--- primer3-1.1.4.orig/debian/README.Debian
+++ primer3-1.1.4/debian/README.Debian
@@ -0,0 +1,9 @@
+Primer3 for Debian
+------------------
+
+The tests included in the sources of Primer3 are ran during the building
+process. You can check the logs at the following address:
+
+http://buildd.debian.org/build.cgi?pkg=primer3
+
+ -- Charles Plessy <charles-debian-nospam@plessy.org>  Tue, 12 Feb 2008 23:22:04 +0900
--- primer3-1.1.4.orig/debian/primer3_core.1.xml
+++ primer3-1.1.4/debian/primer3_core.1.xml
@@ -0,0 +1,153 @@
+<?xml version='1.0' encoding='UTF-8'?>
+<?xml-stylesheet type="text/xsl"
+        href="http://docbook.sourceforge.net/release/xsl/current/manpages/docbook.xsl"?>
+<!DOCTYPE refentry PUBLIC "-//OASIS//DTD DocBook XML V4.5//EN"
+        "http://www.oasis-open.org/docbook/xml/4.5/docbookx.dtd" [
+  <!ENTITY dhfirstname "<firstname>Steffen</firstname>">
+  <!ENTITY dhsurname   "<surname>Moeller</surname>">
+  <!-- Please adjust the date whenever revising the manpage. -->
+  <!ENTITY dhtitle     "Primer3 User Manuals">
+  <!ENTITY dhsection   "<manvolnum>1</manvolnum>">
+  <!ENTITY dhemail     "<email>moeller@debian.org</email>">
+  <!ENTITY dhusername  "Steffen Moeller">
+  <!ENTITY dhucpackage "<refentrytitle>PRIMER3_CORE</refentrytitle>">
+  <!ENTITY dhpackage   "primer3_core">
+  <!ENTITY dhrelease   "1.1.4">
+  <!ENTITY debian      "<productname>Debian</productname>">
+  <!ENTITY gnu         "<acronym>GNU</acronym>">
+  <!ENTITY gpl         "&gnu; <acronym>GPL</acronym>">
+]>
+
+<refentry>
+  <refentryinfo>
+    <title>&dhtitle;</title>
+    <productname>&dhpackage;</productname>
+    <releaseinfo role="version">&dhrelease;</releaseinfo>
+    <address>
+      &dhemail;
+    </address>
+<!--   <author>
+      &dhfirstname;
+      &dhsurname;
+    </author> -->
+    <copyright>
+      <year>1996,1997,1998,1999,2000,2001,2004,2006,2007,2008</year>
+      <holder>Whitehead Institute for Biomedical Research</holder>
+      <holder>Steve Rozen (http://jura.wi.mit.edu/rozen)</holder>
+      <holder>Helen Skaletsky</holder>
+    </copyright>
+    
+    <legalnotice>
+      <para>All rights reserved. On Debian-based systems, please consult <filename>/usr/share/doc/primer3/copyright</filename> to read the licence of &dhpackage;.</para>
+    </legalnotice>
+    
+    <legalnotice>
+      <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 same terms as &dhpackage; itself.<!-- This also applies to this source document --></para>
+    </legalnotice>
+  </refentryinfo>
+  <refmeta>
+    &dhucpackage;
+
+    &dhsection;
+  </refmeta>
+  <refnamediv>
+    <refname>&dhpackage;</refname>
+
+    <refpurpose>Designs primers for PCR</refpurpose>
+  </refnamediv>
+  <refsynopsisdiv>
+    <cmdsynopsis>
+      <command>&dhpackage;</command>
+        <arg choice="opt">-format_output</arg>
+  <!--      <arg choice="opt">-2x_compat</arg>   -->
+        <arg choice="opt">-strict_tags</arg>
+        <arg choice="opt">&lt; <replaceable>input_file</replaceable></arg>
+    </cmdsynopsis>
+  </refsynopsisdiv>
+  
+  <refsect1>
+    <title>DESCRIPTION</title>
+
+    <para>
+      &dhpackage; picks primers for PCR reactions, considering as criteria oligonucleotide melting temperature, size, GC content and primer-dimer possibilities, PCR product size, positional constraints within the source sequence, and miscellaneous other constraints.
+    </para>
+    <para>
+      By default, &dhpackage; accepts input and produces output in Boulder-io format, a pre-XML text-based input/output format for program-to-program data interchange format. The Boulder-io format and the commands that &dhpackage; understands are described in the <filename>README</filename> file, which on Debian systems can be found in <filename class="directory">/usr/share/doc/primer3/</filename>.
+    </para>
+  </refsect1>
+    
+  <refsect1>
+    <title>OPTIONS</title>
+
+    <variablelist>
+      <varlistentry>
+        <term>
+          <option>-format_output</option>
+        </term>
+        <listitem>
+          <para> Prints a more user-oriented report for each sequence.</para>
+        </listitem>
+      </varlistentry>
+<!--
+      <varlistentry>
+        <term>
+          <option>-2x_compat</option>
+        </term>
+        <listitem>
+          <para>Print the output using Primer v2 compatible tag names.</para>
+        </listitem>
+      </varlistentry>
+-->
+    <varlistentry>
+        <term>
+          <option>-strict_tags</option>
+        </term>
+        <listitem>
+          <para>
+            &dhpackage; echoes and ignores any tags it does not recognize, unless the <option>-strict_tags</option> flag is set on the command line, in which case &dhpackage; prints an error in the PRIMER_ERROR output tag, and prints additional information on stdout; this option can be useful for debugging systems that incorporate primer.
+          </para>
+        </listitem>
+      </varlistentry>
+    </variablelist>
+    
+    <note><para>The old flag -2x_compat is no longer supported.</para></note>
+  </refsect1>
+  
+  <refsect1>
+    <title>EXIT STATUS CODES</title>
+    <itemizedlist>
+      <listitem><para> 0 on normal operation.</para></listitem>
+      <listitem><para>-1 under the following conditions: illegal command-line arguments, unable to fflush stdout, unable to open (for writing and creating) a .for, .rev or .int file (probably due to a protection problem).</para></listitem>
+      <listitem><para>-2 on out-of-memory.</para></listitem>
+      <listitem><para>-3 empty input.</para></listitem>
+      <listitem><para>-4 error in a "Global" input tag (message in PRIMER_ERROR).</para></listitem>
+    </itemizedlist>
+  </refsect1>
+
+  <refsect1>
+    <title>REFERENCE</title>
+    <para>
+    Please cite Rozen, S., Skaletsky, H.  "Primer3 on the WWW for general users  and for biologist programmers."  In S. Krawetz and S. Misener, eds. Bioinformatics Methods and Protocols in the series Methods in Molecular Biology.  Humana Press, Totowa, NJ, 2000, pages 365-386.
+    </para>
+  </refsect1>
+
+  <refsect1>
+    <title>SEE ALSO</title>
+    <para>
+      <citerefentry>
+        <refentrytitle>ntdpal</refentrytitle>
+        <manvolnum>1</manvolnum>
+      </citerefentry>
+      
+      <citerefentry>
+        <refentrytitle>oligotm</refentrytitle>
+        <manvolnum>1</manvolnum>
+      </citerefentry>
+    </para>
+  </refsect1>
+
+</refentry>
+
--- primer3-1.1.4.orig/debian/rules
+++ primer3-1.1.4/debian/rules
@@ -0,0 +1,11 @@
+#!/usr/bin/make -f
+
+include /usr/share/cdbs/1/class/makefile.mk
+include /usr/share/cdbs/1/rules/debhelper.mk
+
+DEB_MAKE_CHECK_TARGET   = -C test test
+DEB_MAKE_CLEAN_TARGET   = -C src clean
+DEB_MAKE_BUILD_TARGET   = -C src all
+
+clean::
+	$(MAKE) -C test clean
--- primer3-1.1.4.orig/debian/ntdpal.1.xml
+++ primer3-1.1.4/debian/ntdpal.1.xml
@@ -0,0 +1,222 @@
+<?xml version='1.0' encoding='UTF-8'?>
+<?xml-stylesheet type="text/xsl"
+        href="http://docbook.sourceforge.net/release/xsl/current/manpages/docbook.xsl"?>
+<!DOCTYPE refentry PUBLIC "-//OASIS//DTD DocBook XML V4.5//EN"
+        "http://www.oasis-open.org/docbook/xml/4.5/docbookx.dtd" [
+  <!ENTITY dhfirstname "<firstname>Charles</firstname>">
+  <!ENTITY dhsurname   "<surname>Plessy</surname>">
+  <!ENTITY dhsection   "<manvolnum>1</manvolnum>">
+  <!ENTITY dhemail     "<email>plessy@debian.org</email>">
+  <!ENTITY dhusername  "Charles Plessy">
+  <!ENTITY dhtitle     "Primer3 User Manuals">
+  <!ENTITY dhucpackage "<refentrytitle>NTDPAL</refentrytitle>">
+  <!ENTITY dhpackage   "ntdpal">
+  <!ENTITY dhrelease   "1.1.4">
+  <!ENTITY debian      "<productname>Debian</productname>">
+  <!ENTITY gnu         "<acronym>GNU</acronym>">
+  <!ENTITY gpl         "&gnu; <acronym>GPL</acronym>">
+]>
+
+<refentry>
+  <refentryinfo>
+    <title>&dhtitle;</title>
+    <productname>&dhpackage;</productname>
+    <releaseinfo role="version">&dhrelease;</releaseinfo>
+    <address>
+      &dhemail;
+    </address>
+  <!--   <author>
+      &dhfirstname;
+      &dhsurname;
+    </author> -->
+    <copyright>
+      <year>1996,1997,1998,1999,2000,2001,2004,2006,2007,2008</year>
+      <holder>Whitehead Institute for Biomedical Research</holder>
+      <holder>Steve Rozen (http://jura.wi.mit.edu/rozen)</holder>
+      <holder>Helen Skaletsky</holder>
+    </copyright>
+    
+    <legalnotice>
+      <para>All rights reserved. On Debian-based systems, please consult <filename>/usr/share/doc/primer3/copyright</filename> to read the licence of &dhpackage;.</para>
+    </legalnotice>
+    
+    <legalnotice>
+      <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 same terms as oligotm itself.<!-- This also applies to this source document --></para>
+    </legalnotice>
+  </refentryinfo>
+  
+  <refmeta>
+    &dhucpackage;
+    &dhsection;
+  </refmeta>
+  
+  <refnamediv>
+    <refname>&dhpackage;</refname>
+
+    <refpurpose>Provides Primer3's alignment functionality</refpurpose>
+  </refnamediv>
+  <refsynopsisdiv>
+    <cmdsynopsis>
+      <command>&dhpackage;</command>
+      <arg choice="opt">
+        -g <replaceable class="parameter">gval</replaceable>
+      </arg>
+     	<arg choice="opt">
+        -l <replaceable class="parameter">lval</replaceable>
+      </arg>
+      <arg choice="opt">
+        -m <replaceable class="parameter">mval</replaceable>
+      </arg>
+      <arg choice="opt">-f1, f2, f3</arg>
+    	<arg choice="opt">-p</arg>
+    	<arg choice="opt">-s</arg>
+     <arg choice="opt">-e</arg>
+     <arg choice="req">
+       <replaceable class="parameter">seq1</replaceable>
+      </arg>
+     <arg choice="req">
+       <replaceable class="parameter">seq2</replaceable>
+     </arg>
+     <arg choice="req"><replaceable class="parameter">mode</replaceable></arg>
+    </cmdsynopsis>
+  </refsynopsisdiv>
+  <refsect1>
+    <title>DESCRIPTION</title>
+
+    <para>
+      Ntdpal (NucleoTide Dynamic Programming ALignment) is a stand-alone program
+      that provides Primer3's alignment functionality (local, a.k.a.
+      Smith-Waterman, global, a.k.a. Needleman-Wunsch, plus "half global").
+    </para>
+  </refsect1>
+  
+  <refsect1>
+    <title>OPTIONS</title>
+
+    <variablelist>
+      <varlistentry>
+        <term>
+          <option>-g</option> <parameter>gval</parameter>
+        </term>
+        <listitem>
+          <para><parameter>gval</parameter> is a (positive) float (.01 precision) specifying penaltiy for creating a gap respectively (the penalties are subtracted from the output score)</para>
+        </listitem>
+      </varlistentry>
+
+      <varlistentry>
+        <term>
+          <option>-l</option> <parameter>val</parameter>
+        </term>
+        <listitem>
+          <para><parameter>lval</parameter> is a (positive) float (.01 precision) specifying penaltiy for lengthening a gap respectively (the penalties are subtracted from the output score)</para>
+        </listitem>
+      </varlistentry>
+ 
+    <varlistentry>
+        <term>
+          <option>-a</option>
+        </term>
+        <listitem>
+          <para>Causes the scoring matrix to be modified by dpal_set_ambiguity_codes.</para>
+        </listitem>
+      </varlistentry>
+
+     <varlistentry>
+        <term>
+          <option>-e</option>
+        </term>
+        <listitem>
+          <para>Causes the end postion of the alignment in both sequences to be printed. Do not confuse with the 'e' <emphasis>mode</emphasis>.</para>
+        </listitem>
+      </varlistentry>
+
+     <varlistentry>
+        <term>
+          <option>-f1, -f2, -f3</option>
+        </term>
+        <listitem>
+          <para>Force specific implementations. -f2 forces use an implementation that might provide more informative error messages, possibly at the expense of some speed.</para>
+        </listitem>
+      </varlistentry>
+
+     <varlistentry>
+        <term>
+          <option>-h</option>
+        </term>
+        <listitem>
+          <para>Use a different scoring matrix: G and C matches = 3, A and T = 2, and mismatches = -0.5. (The default scoring matrix assigns 1 to a match, and -1 to a mismatch.)
+         </para>
+        </listitem>
+      </varlistentry>
+
+    <varlistentry>
+        <term>
+          <option>-p</option>
+        </term>
+        <listitem>
+          <para>Causes the alignment to be displayed on stderr.</para>
+        </listitem>
+      </varlistentry>
+
+     <varlistentry>
+        <term>
+          <option>-s</option>
+        </term>
+        <listitem>
+          <para>causes <emphasis>only</emphasis> the score to printed.</para>
+        </listitem>
+      </varlistentry>
+
+     <varlistentry>
+        <term>
+          <option>-m</option> <parameter>mval</parameter>
+        </term>
+        <listitem>
+          <para>is the maximum allowed gap (default is 3).</para>
+        </listitem>
+      </varlistentry>
+
+     <varlistentry>
+        <term>
+	        <replaceable>seq1</replaceable> and <replaceable>seq2</replaceable>
+        </term>
+        <listitem>
+          <para>are the sequences to be aligned.</para>
+        </listitem>
+      </varlistentry>
+
+      <varlistentry>
+        <term>
+	        <replaceable>mode</replaceable>
+	      </term>
+        <listitem>
+          <para> is one of <parameter>g</parameter>, <parameter>G</parameter>, <parameter>l</parameter>, or <parameter>L</parameter> specifying a global, global end-anchored, local, or local end-achored alignment respectively.  For backward compatibility <parameter>e</parameter> is equivalent to <parameter>G</parameter>.</para>
+        </listitem>
+      </varlistentry>
+    </variablelist>
+  </refsect1>
+
+  <refsect1>
+    <title>REFERENCE</title>
+    <para>
+      Please cite Rozen, S., Skaletsky, H.  "Primer3 on the WWW for general users and for biologist programmers."  In S. Krawetz and S. Misener, eds. Bioinformatics Methods and Protocols in the series Methods in Molecular Biology.  Humana Press, Totowa, NJ, 2000, pages 365-386.
+    </para> 
+  </refsect1>
+  
+  <refsect1>
+    <title>SEE ALSO</title>
+    <para>
+      <citerefentry>
+        <refentrytitle>primer3_core</refentrytitle>
+        <manvolnum>1</manvolnum>
+      </citerefentry>
+      <citerefentry>
+        <refentrytitle>oligotm</refentrytitle>
+        <manvolnum>1</manvolnum>
+      </citerefentry>
+    </para>
+  </refsect1>
+</refentry>
--- primer3-1.1.4.orig/debian/ntdpal.1
+++ primer3-1.1.4/debian/ntdpal.1
@@ -0,0 +1,112 @@
+.\"     Title: NTDPAL
+.\"    Author: 
+.\" Generator: DocBook XSL Stylesheets v1.73.2 <http://docbook.sf.net/>
+.\"      Date: 05/09/2008
+.\"    Manual: Primer3 User Manuals
+.\"    Source: ntdpal 1.1.4
+.\"
+.TH "NTDPAL" "1" "05/09/2008" "ntdpal 1.1.4" "Primer3 User Manuals"
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.SH "NAME"
+ntdpal \- Provides Primer3's alignment functionality
+.SH "SYNOPSIS"
+.HP 7
+\fBntdpal\fR [\-g\ \fIgval\fR] [\-l\ \fIlval\fR] [\-m\ \fImval\fR] [\-f1,\ f2,\ f3] [\-p] [\-s] [\-e] {\fIseq1\fR} {\fIseq2\fR} {\fImode\fR}
+.SH "DESCRIPTION"
+.PP
+Ntdpal (NucleoTide Dynamic Programming ALignment) is a stand\-alone program that provides Primer3\'s alignment functionality (local, a\&.k\&.a\&. Smith\-Waterman, global, a\&.k\&.a\&. Needleman\-Wunsch, plus "half global")\&.
+.SH "OPTIONS"
+.PP
+\fB\-g\fR \fIgval\fR
+.RS 4
+\fIgval\fR
+is a (positive) float (\&.01 precision) specifying penaltiy for creating a gap respectively (the penalties are subtracted from the output score)
+.RE
+.PP
+\fB\-l\fR \fIval\fR
+.RS 4
+\fIlval\fR
+is a (positive) float (\&.01 precision) specifying penaltiy for lengthening a gap respectively (the penalties are subtracted from the output score)
+.RE
+.PP
+\fB\-a\fR
+.RS 4
+Causes the scoring matrix to be modified by dpal_set_ambiguity_codes\&.
+.RE
+.PP
+\fB\-e\fR
+.RS 4
+Causes the end postion of the alignment in both sequences to be printed\&. Do not confuse with the \'e\'
+\fImode\fR\&.
+.RE
+.PP
+\fB\-f1, \-f2, \-f3\fR
+.RS 4
+Force specific implementations\&. \-f2 forces use an implementation that might provide more informative error messages, possibly at the expense of some speed\&.
+.RE
+.PP
+\fB\-h\fR
+.RS 4
+Use a different scoring matrix: G and C matches = 3, A and T = 2, and mismatches = \-0\&.5\&. (The default scoring matrix assigns 1 to a match, and \-1 to a mismatch\&.)
+.RE
+.PP
+\fB\-p\fR
+.RS 4
+Causes the alignment to be displayed on stderr\&.
+.RE
+.PP
+\fB\-s\fR
+.RS 4
+causes
+\fIonly\fR
+the score to printed\&.
+.RE
+.PP
+\fB\-m\fR \fImval\fR
+.RS 4
+is the maximum allowed gap (default is 3)\&.
+.RE
+.PP
+\fIseq1\fR and \fIseq2\fR
+.RS 4
+are the sequences to be aligned\&.
+.RE
+.PP
+\fImode\fR
+.RS 4
+is one of
+\fIg\fR,
+\fIG\fR,
+\fIl\fR, or
+\fIL\fR
+specifying a global, global end\-anchored, local, or local end\-achored alignment respectively\&. For backward compatibility
+\fIe\fR
+is equivalent to
+\fIG\fR\&.
+.RE
+.SH "REFERENCE"
+.PP
+Please cite Rozen, S\&., Skaletsky, H\&. "Primer3 on the WWW for general users and for biologist programmers\&." In S\&. Krawetz and S\&. Misener, eds\&. Bioinformatics Methods and Protocols in the series Methods in Molecular Biology\&. Humana Press, Totowa, NJ, 2000, pages 365\-386\&.
+.SH "SEE ALSO"
+.PP
+
+\fBprimer3_core\fR(1)
+\fBoligotm\fR(1)
+.SH "COPYRIGHT"
+Copyright \(co 1996,1997,1998,1999,2000,2001,2004,2006,2007,2008 Whitehead Institute for Biomedical Research, Steve Rozen (http://jura.wi.mit.edu/rozen), Helen Skaletsky
+.br
+.PP
+All rights reserved\&. On Debian\-based systems, please consult
+\fI/usr/share/doc/primer3/copyright\fR
+to read the licence of ntdpal\&.
+.PP
+This manual page was written by Charles Plessy
+<plessy@debian\&.org>
+for the
+Debian(TM)
+system (but may be used by others)\&. Permission is granted to copy, distribute and/or modify this document under the same terms as oligotm itself\&.
+
+.sp
--- primer3-1.1.4.orig/debian/control
+++ primer3-1.1.4/debian/control
@@ -0,0 +1,33 @@
+Source: primer3
+Section: science
+Priority: optional
+Maintainer: Debian-Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
+DM-Upload-Allowed: yes
+Uploaders: Steffen Moeller <moeller@debian.org>,
+ Charles Plessy <plessy@debian.org>,
+ David Paleino <d.paleino@gmail.com>
+Build-Depends: debhelper (>= 5), cdbs
+Standards-Version: 3.7.3
+Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/primer3/trunk/?rev=0&sc=0
+Vcs-Svn: svn://svn.debian.org/svn/debian-med/trunk/packages/primer3/trunk/
+Homepage: http://primer3.sourceforge.net
+
+Package: primer3
+Architecture: any
+Depends: ${shlibs:Depends}, ${misc:Depends} 
+Suggests: ncbi-epcr
+Enhances: emboss
+Description: Tool to design flanking oligo nucleotides for DNA amplification
+ Primer3 picks primers for Polymerase Chain Reactions (PCRs), considering as
+ criteria oligonucleotide melting temperature, size, GC content and
+ primer-dimer possibilities, PCR product size, positional constraints within
+ the source sequence, and miscellaneous other constraints. All of these
+ criteria are user-specifiable as constraints, and some are specifiable as
+ terms in an objective function that characterizes an optimal primer pair.
+ .
+ It has been published in Rozen S and Skaletsky H, "Primer3 on the WWW for
+ general users and for biologist programmers.", Methods Mol Biol.
+ 2000;132:365-86. 
+ .
+ The Whitehead Institute for Biomedical Research provides a web-based
+ front end to Primer3.
--- primer3-1.1.4.orig/debian/primer3.manpages
+++ primer3-1.1.4/debian/primer3.manpages
@@ -0,0 +1,3 @@
+debian/ntdpal.1
+debian/primer3_core.1
+debian/oligotm.1
--- primer3-1.1.4.orig/debian/primer3.examples
+++ primer3-1.1.4/debian/primer3.examples
@@ -0,0 +1 @@
+example
--- primer3-1.1.4.orig/debian/changelog
+++ primer3-1.1.4/debian/changelog
@@ -0,0 +1,84 @@
+primer3 (1.1.4-1) unstable; urgency=low
+
+  * New upstream release (No changes on Linux systems).
+  * Updated my email address (debian/control, debian/copyright, manpages).
+  * Updated the manpages:
+    - using DocBook 4.5
+    - incremented Primer3 version to 1.1.4
+
+ -- Charles Plessy <plessy@debian.org>  Fri, 09 May 2008 12:54:28 +0900
+
+primer3 (1.1.3-1) unstable; urgency=low
+
+  [ Charles Plessy ]
+  * New upstream version:
+    - 1.1.3: Corrected static buffer overflow errors in
+      boulder_print_pairs() and boulder_print_oligos() in primer3_main.c.
+    - 1.1.2: Updates to dpal.c so that no error forces an exit.
+      Adpatation in primer3_main.c and ntdpal_main.c to
+        updated error handling in dpal().
+      Arranged for primer3_main.c align() to check for
+        and circumvent local alignments to "targets" < 3 nucleotides
+        long, and added tests for this condition.
+      Comment and code readability updates in dpal.h and dpal.c
+  * Moved the Homepage: field out from the package's description.
+  * debian/control: updated Steffen's email address.
+  * debian/*.1.xml: corrected the headers of the sources of manpages.
+  * debian/rules: converted to CDBS.
+
+  [ David Paleino ]
+  * debian/ntdpal.1, debian/primer3_core.1 and debian/oligotm.1
+    added - manpages are statically built now
+  * debian/control:
+    - B-D updated
+    - added myself to Uploaders
+  * Updated to Standards-Version 3.7.3 (no changes needed)
+
+ -- Charles Plessy <charles-debian-nospam@plessy.org>  Mon, 25 Feb 2008 16:31:58 +0900
+
+primer3 (1.1.1-1) unstable; urgency=low
+
+  * New upstream release.
+  * Enhances: emboss because EMBOSS has a wrapper for primer3_core.
+  * Add Subversion repository URL to debian/control.
+  * Updated the manpages
+
+ -- Charles Plessy <charles-debian-nospam@plessy.org>  Sun,  3 Jun 2007 16:16:19 +0900
+
+primer3 (1.1.0~beta-1) experimental; urgency=low
+
+  * New upstream release.
+    - Some part of primer3 is now licenced under the GNU GPL.
+    - The oligtotm() function is now provided as a library, liboligotm.
+    - The oligotm executable now takes additional arguments.
+    - Non-backward compatible change: removed support of flag -2x_compat.
+  * Added a watch file now that the sources are hosted on SourceForge.net.
+  * Updated manpages.
+
+ -- Charles Plessy <charles-debian-nospam@plessy.org>  Sun, 18 Feb 2007 09:04:16 +0900
+
+primer3 (1.0b-1) unstable; urgency=low
+
+  * Initial release. (Closes: #241235)
+  * New upstream version released under a revised BSD licence.
+  * Swiching to collaborative maintainance: Maintainer is a mailing-list,
+    Uploaders are real people.
+  * Using debhelper v5 and conforming to policy 3.7.2.
+  * Relicencing the manpage of Primer3 (thanks to Steffen Moeller), adding one
+    for ntdpal and oligotm.
+  * Extensive tests during bulding, except on slow architectures.
+
+ -- Charles Plessy <charles-debian-nospam@plessy.org>  Thu, 28 Sep 2006 20:18:54 +0900
+
+primer3 (0.9-0.2) unstable; urgency=low
+  
+  * Contacted upstream author, change of section to non-free/optional.
+
+ -- Steffen Moeller <moeller@pzr.uni-rostock.de>  Wed,  1 Apr 2004 15:07:10 +0200
+ 
+primer3 (0.9-0.1) unstable; urgency=low
+
+  * Pre-Release.
+
+ -- Steffen Moeller <moeller@pzr.uni-rostock.de>  Wed, 31 Mar 2004 15:07:10 +0200
+
--- primer3-1.1.4.orig/debian/primer3_core.1
+++ primer3-1.1.4/debian/primer3_core.1
@@ -0,0 +1,90 @@
+.\"     Title: PRIMER3_CORE
+.\"    Author: 
+.\" Generator: DocBook XSL Stylesheets v1.73.2 <http://docbook.sf.net/>
+.\"      Date: 05/09/2008
+.\"    Manual: Primer3 User Manuals
+.\"    Source: primer3_core 1.1.4
+.\"
+.TH "PRIMER3_CORE" "1" "05/09/2008" "primer3_core 1.1.4" "Primer3 User Manuals"
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.SH "NAME"
+primer3_core \- Designs primers for PCR
+.SH "SYNOPSIS"
+.HP 13
+\fBprimer3_core\fR [\-format_output] [\-strict_tags] [<\ \fIinput_file\fR]
+.SH "DESCRIPTION"
+.PP
+primer3_core picks primers for PCR reactions, considering as criteria oligonucleotide melting temperature, size, GC content and primer\-dimer possibilities, PCR product size, positional constraints within the source sequence, and miscellaneous other constraints\&.
+.PP
+By default, primer3_core accepts input and produces output in Boulder\-io format, a pre\-XML text\-based input/output format for program\-to\-program data interchange format\&. The Boulder\-io format and the commands that primer3_core understands are described in the
+\fIREADME\fR
+file, which on Debian systems can be found in
+\fI/usr/share/doc/primer3/\fR\&.
+.SH "OPTIONS"
+.PP
+\fB\-format_output\fR
+.RS 4
+Prints a more user\-oriented report for each sequence\&.
+.RE
+.PP
+\fB\-strict_tags\fR
+.RS 4
+primer3_core echoes and ignores any tags it does not recognize, unless the
+\fB\-strict_tags\fR
+flag is set on the command line, in which case primer3_core prints an error in the PRIMER_ERROR output tag, and prints additional information on stdout; this option can be useful for debugging systems that incorporate primer\&.
+.RE
+.sp
+.it 1 an-trap
+.nr an-no-space-flag 1
+.nr an-break-flag 1
+.br
+Note
+.PP
+The old flag \-2x_compat is no longer supported\&.
+.SH "EXIT STATUS CODES"
+.sp
+.RS 4
+\h'-04'\(bu\h'+03'0 on normal operation\&.
+.RE
+.sp
+.RS 4
+\h'-04'\(bu\h'+03'\-1 under the following conditions: illegal command\-line arguments, unable to fflush stdout, unable to open (for writing and creating) a \&.for, \&.rev or \&.int file (probably due to a protection problem)\&.
+.RE
+.sp
+.RS 4
+\h'-04'\(bu\h'+03'\-2 on out\-of\-memory\&.
+.RE
+.sp
+.RS 4
+\h'-04'\(bu\h'+03'\-3 empty input\&.
+.RE
+.sp
+.RS 4
+\h'-04'\(bu\h'+03'\-4 error in a "Global" input tag (message in PRIMER_ERROR)\&.
+.RE
+.SH "REFERENCE"
+.PP
+Please cite Rozen, S\&., Skaletsky, H\&. "Primer3 on the WWW for general users and for biologist programmers\&." In S\&. Krawetz and S\&. Misener, eds\&. Bioinformatics Methods and Protocols in the series Methods in Molecular Biology\&. Humana Press, Totowa, NJ, 2000, pages 365\-386\&.
+.SH "SEE ALSO"
+.PP
+
+\fBntdpal\fR(1)
+\fBoligotm\fR(1)
+.SH "COPYRIGHT"
+Copyright \(co 1996,1997,1998,1999,2000,2001,2004,2006,2007,2008 Whitehead Institute for Biomedical Research, Steve Rozen (http://jura.wi.mit.edu/rozen), Helen Skaletsky
+.br
+.PP
+All rights reserved\&. On Debian\-based systems, please consult
+\fI/usr/share/doc/primer3/copyright\fR
+to read the licence of primer3_core\&.
+.PP
+This manual page was written by Steffen Moeller
+<moeller@debian\&.org>
+for the
+Debian(TM)
+system (but may be used by others)\&. Permission is granted to copy, distribute and/or modify this document under the same terms as primer3_core itself\&.
+
+.sp
--- primer3-1.1.4.orig/debian/oligotm.1
+++ primer3-1.1.4/debian/oligotm.1
@@ -0,0 +1,114 @@
+.\"     Title: OLIGOTM
+.\"    Author: 
+.\" Generator: DocBook XSL Stylesheets v1.73.2 <http://docbook.sf.net/>
+.\"      Date: 05/09/2008
+.\"    Manual: Primer3 User Manuals
+.\"    Source: oligotm 1.1.4
+.\"
+.TH "OLIGOTM" "1" "05/09/2008" "oligotm 1.1.4" "Primer3 User Manuals"
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.SH "NAME"
+oligotm \- Prints oligo's melting temperature on stdout
+.SH "SYNOPSIS"
+.HP 8
+\fBoligotm\fR [OPTIONS] {oligo}
+.PP
+where oligo is a DNA sequence of between 2 and 36 bases
+.SH "DESCRIPTION"
+.PP
+
+\fBoligotm\fR
+prints the melting temperature of a given desoxyribooligonucleotide on the standard output\&. It is part of the oligotm library\&.
+.SH "OPTIONS"
+.PP
+\fB\-mv\fR \fImonovalent_conc\fR
+.RS 4
+Concentration of monovalent cations in mM, by default 50\ \&mM\&.
+.RE
+.PP
+\fB\-dv\fR \fIdivalent_conc\fR
+.RS 4
+Concentration of divalent cations in mM, by default 0\ \&mM\&.
+.RE
+.PP
+\fB\-n\fR \fIdNTP_conc\fR
+.RS 4
+Concentration of deoxynycleotide triphosphate in mM, by default 0\ \&mM\&.
+.RE
+.PP
+\fB\-d\fR \fIdna_conc\fR
+.RS 4
+Concentration of DNA strands in nM, by default 50\ \&nM\&.
+.RE
+.PP
+\fB\-tp\fR \fI[0|1]\fR
+.RS 4
+Specifies the table of thermodynamic parameters and the method of melting temperature calculation:
+.sp
+.RS 4
+\h'-04'\(bu\h'+03'\fI0\fR
+Breslauer et al\&., 1986 and Rychlik et al\&., 1990 (used by primer3 up to and including release 1\&.1\&.0)\&. This is the default, but
+\fInot\fR
+the recommended value\&.
+.RE
+.sp
+.RS 4
+\h'-04'\(bu\h'+03'\fI1\fR
+Use nearest neighbor parameter from SantaLucia 1998\&.
+\fIThis is the recommended value\fR\&.
+.RE
+.RE
+.PP
+\fB\-sc\fR \fI[0\&.\&.2]\fR
+.RS 4
+Specifies salt correction formula for the melting temperature calculation:
+.sp
+.RS 4
+\h'-04'\(bu\h'+03'\fI0\fR
+Schildkraut and Lifson 1965, used by primer3 up to and including release 1\&.1\&.0\&. This is the default, but
+\fInot\fR
+the recommended value\&.
+.RE
+.sp
+.RS 4
+\h'-04'\(bu\h'+03'\fI1\fR
+SantaLucia 1998\&.
+\fIThis is the recommended value\fR\&.
+.RE
+.sp
+.RS 4
+\h'-04'\(bu\h'+03'\fI1\fR
+Owczarzy et al\&., 2004\&.
+.RE
+.RE
+.PP
+\fB\-i\fR
+.RS 4
+prints references to publications which were used for thermodynamic calculations\&.
+.RE
+.SH "REFERENCE"
+.PP
+Please cite Rozen, S\&., Skaletsky, H\&. "Primer3 on the WWW for general users and for biologist programmers\&." In S\&. Krawetz and S\&. Misener, eds\&. Bioinformatics Methods and Protocols in the series Methods in Molecular Biology\&. Humana Press, Totowa, NJ, 2000, pages 365\-386\&.
+.SH "SEE ALSO"
+.PP
+
+\fBprimer3_core\fR(1)
+\fBntdpal\fR(1)
+.SH "COPYRIGHT"
+Copyright \(co 1996,1997,1998,1999,2000,2001,2004,2006,2007,2008 Whitehead Institute for Biomedical Research, Steve Rozen (http://jura.wi.mit.edu/rozen), Helen Skaletsky
+.br
+.PP
+All rights reserved\&. On Debian\-based systems, please consult
+\fI/usr/share/doc/primer3/copyright\fR
+to read the licence of oligotm\&.
+.PP
+This manual page was written by Charles Plessy
+<plessy@debian\&.org>
+for the
+Debian(TM)
+system (but may be used by others)\&. Permission is granted to copy, distribute and/or modify this document under the same terms as oligotm itself\&.
+
+.sp
--- primer3-1.1.4.orig/debian/primer3.docs
+++ primer3-1.1.4/debian/primer3.docs
@@ -0,0 +1,3 @@
+README.txt
+src/release_notes.txt
+how-to-cite.txt
--- primer3-1.1.4.orig/debian/copyright
+++ primer3-1.1.4/debian/copyright
@@ -0,0 +1,67 @@
+Format-Specification: http://wiki.debian.org/Proposals/CopyrightFormat?action=recall&rev=103
+Debianized-By: Steffen Möller <moeller@debian.org>
+Debianized-Date: Wed, 31 Mar 2004 15:07:10 +0200
+Original-Source-Location: http://downloads.sourceforge.net/primer3/primer3-1.1.4.tar.gz
+Upstream-Author: Steve Rozen and Helen Skaletsky
+
+Files: *
+Copyright: © 1996,1997,1998,1999,2000,2001,2004,2006,2007,2008
+           Whitehead Institute for Biomedical Research,
+	   Steve Rozen (http://jura.wi.mit.edu/rozen),
+	   Helen Skaletsky
+License: BSD family
+ Redistribution and use in source and binary forms, with or without
+ modification, are permitted provided that the following conditions are
+ met:
+ .
+    * Redistributions of source code must retain the above copyright
+ notice, this list of conditions and the following disclaimer.
+    * 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.
+    * Neither the names of the copyright holders nor contributors may
+ be used to endorse or promote products derived from this software
+ without specific prior written permission.
+ .
+ THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS 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 COPYRIGHT
+ OWNERS 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.
+
+Files: src/oligotm*, tst/oligotm_test.pl
+Copyright: © 1996,1997,1998,1999,2000,2001,2004,2006,2007,2008
+           Whitehead Institute for Biomedical Research,
+           Steve Rozen (http://jura.wi.mit.edu/rozen),
+	   Helen Skaletsky
+License: GPL-2+
+ The oligotm library 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.
+ .
+ The oligotm library is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ GNU General Public License for more details.
+ .
+ You should have received a copy of the GNU General Public License
+ along with this package; if not, write to the Free Software
+ Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA  02110-1301 USA
+X-Comment: On Debian systems, the complete text of the GNU General
+Public License can be found in `/usr/share/common-licenses/GPL'.
+
+Files: debian/*
+Copyright: © 2004 Steffen Möller <moeller@debian.org>
+           © 2006-2008 Charles Plessy <plessy@debian.org>
+           © 2008 David Paleino <d.paleino@gmail.com>
+License: PD
+ The packaging work is hereby released in the public domain unless stated
+ otherwise.