[med-svn] r212 - trunk/packages/primer3/trunk/debian
Charles Plessy
charles-guest at alioth.debian.org
Sat Feb 17 10:11:57 CET 2007
Author: charles-guest
Date: 2007-02-17 10:11:56 +0100 (Sat, 17 Feb 2007)
New Revision: 212
Modified:
trunk/packages/primer3/trunk/debian/changelog
trunk/packages/primer3/trunk/debian/copyright
trunk/packages/primer3/trunk/debian/ntdpal.1.xml
trunk/packages/primer3/trunk/debian/oligotm.1.xml
trunk/packages/primer3/trunk/debian/primer3.docs
trunk/packages/primer3/trunk/debian/primer3_core.1.xml
trunk/packages/primer3/trunk/debian/rules
Log:
Updated manpage, copyrights, and debian/rules
Modified: trunk/packages/primer3/trunk/debian/changelog
===================================================================
--- trunk/packages/primer3/trunk/debian/changelog 2007-02-17 04:31:55 UTC (rev 211)
+++ trunk/packages/primer3/trunk/debian/changelog 2007-02-17 09:11:56 UTC (rev 212)
@@ -1,9 +1,10 @@
-primer3 (1.1.0~beta-1) experimental ; urgency=low
+primer3 (1.1.0~beta-1) experimental; urgency=low
* New upstream release. Some part of primer3 is now licenced under the GNU GPL.
* Added a watch file now that the sources are hosted on SourceForge.net.
+ * Updated manpages.
- -- Charles Plessy <charles-debian-nospam at plessy.org> Sat, 17 Feb 2007 13:16:49 +0900
+ -- Charles Plessy <charles-debian-nospam at plessy.org> Sat, 17 Feb 2007 18:11:12 +0900
primer3 (1.0b-1) unstable; urgency=low
Modified: trunk/packages/primer3/trunk/debian/copyright
===================================================================
--- trunk/packages/primer3/trunk/debian/copyright 2007-02-17 04:31:55 UTC (rev 211)
+++ trunk/packages/primer3/trunk/debian/copyright 2007-02-17 09:11:56 UTC (rev 212)
@@ -1,10 +1,15 @@
-Primer3 is available from: http://fokker.wi.mit.edu/primer3/.
+Primer3 is available from: http://sourceforge.net/projects/primer3/
Copyright (c) 1996,1997,1998,1999,2000,2001,2004,2006
Whitehead Institute for Biomedical Research, Steve Rozen
(http://jura.wi.mit.edu/rozen), and Helen Skaletsky
All rights reserved.
+Most of primer3 is released under the NEW BSD license.
+The oligotm library is released under GNU General Public Licence.
+
+
+--------------------- NEW BSD licence of primer3 -----------------------------
Redistribution and use in source and binary forms, with or without
modification, are permitted provided that the following conditions are
met:
@@ -30,10 +35,30 @@
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.
+-------------------------------------------------------------------------------
+
+-------------- Licence of the oligotm library ---------------------------------
+ This package is free software; you can redistribute it and/or modify
+ it under the terms of the GNU General Public License as published by
+ the Free Software Foundation; either version 2 of the License, or
+ (at your option) any later version.
+
+ This package is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ GNU General Public License for more details.
+
+ You should have received a copy of the GNU General Public License
+ along with this package; if not, write to the Free Software
+ Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA
-------------------------------------------------------------------------------
+On Debian systems, the complete text of the GNU General
+Public License can be found in `/usr/share/common-licenses/GPL'.
+
+
This Debian-packaged version of primer3 was first assembled by Steffen Moeller
<steffen_moeller at gmx.de> on Wed, 31 Mar 2004 15:07:10 +0200. The packaging was
finished in 2006 by Charles Plessy <charles-debian-nospam at plessy.org>. The
Modified: trunk/packages/primer3/trunk/debian/ntdpal.1.xml
===================================================================
--- trunk/packages/primer3/trunk/debian/ntdpal.1.xml 2007-02-17 04:31:55 UTC (rev 211)
+++ trunk/packages/primer3/trunk/debian/ntdpal.1.xml 2007-02-17 09:11:56 UTC (rev 212)
@@ -1,14 +1,16 @@
<?xml version='1.0' encoding='ISO-8859-1'?>
<!DOCTYPE refentry PUBLIC "-//OASIS//DTD DocBook XML V4.4//EN"
"/usr/share/xml/docbook/schema/dtd/4.4/docbookx.dtd" [
- <!ENTITY dhfirstname "<firstname>CHARLES</firstname>">
- <!ENTITY dhsurname "<surname>PLESSY</surname>">
- <!ENTITY dhdate "<date>August 28, 2006</date>">
+ <!ENTITY dhfirstname "<firstname>Charles</firstname>">
+ <!ENTITY dhsurname "<surname>Plessy</surname>">
+ <!ENTITY dhdate "<date>February 17, 2007</date>">
<!ENTITY dhsection "<manvolnum>1</manvolnum>">
<!ENTITY dhemail "<email>charles-debian-nospam at plessy.org</email>">
<!ENTITY dhusername "Charles Plessy">
+ <!ENTITY dhtitle "Primer3 User Manuals">
<!ENTITY dhucpackage "<refentrytitle>NTDPAL</refentrytitle>">
<!ENTITY dhpackage "ntdpal">
+ <!ENTITY dhrelease "1.1.0~beta">
<!ENTITY debian "<productname>Debian</productname>">
<!ENTITY gnu "<acronym>GNU</acronym>">
<!ENTITY gpl "&gnu; <acronym>GPL</acronym>">
@@ -16,6 +18,10 @@
<refentry>
<refentryinfo>
+ <title>&dhtitle;</title>
+ <productname>&dhpackage;</productname>
+ <releaseinfo role="version">&dhrelease;</releaseinfo>
+ &dhdate;
<address>
&dhemail;
</address>
@@ -24,16 +30,29 @@
&dhsurname;
</author> -->
<copyright>
- <year>2006</year>
- <holder>&dhusername;</holder>
+ <year>1996,1997,1998,1999,2000,2001,2004,2006</year>
+ <holder>Whitehead Institute for Biomedical Research</holder>
+ <holder>Steve Rozen (http://jura.wi.mit.edu/rozen)</holder>
+ <holder>Helen Skaletsky</holder>
</copyright>
- &dhdate;
+
+ <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>
@@ -42,16 +61,26 @@
<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">-f2</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>seq2</replaceable></arg>
- <arg choice="req"><replaceable>mode</replaceable></arg>
+ <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>
@@ -73,10 +102,7 @@
<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>
+ <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>
@@ -85,10 +111,7 @@
<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>
+ <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>
@@ -106,8 +129,7 @@
<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>
+ <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>
@@ -116,10 +138,7 @@
<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>
+ <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>
@@ -128,9 +147,7 @@
<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>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>
@@ -164,23 +181,19 @@
<varlistentry>
<term>
- <replaceable>seq1</replaceable> and <replaceable>seq2</replaceable>
+ <replaceable>seq1</replaceable> and <replaceable>seq2</replaceable>
</term>
<listitem>
<para>are the sequences to be aligned.</para>
</listitem>
</varlistentry>
-<varlistentry>
+ <varlistentry>
<term>
- <replaceable>mode</replaceable>
- </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>
+ <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>
@@ -189,54 +202,21 @@
<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.
+ 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>primer3_core (1), oligotm (1)</para>
-
- </refsect1>
- <refsect1>
- <title>COPYRIGHTS</title>
-
<para>
- Copyright (c) 1996,1997,1998,1999,2000,2001,2004,2006 Steve Rozen, Helen Skaletsky, and Whitehead
- Institute for Biomedical Research. On Debian-based systems, please consult
- <filename>/usr/share/doc/primer3/copyright</filename> to read the licence
- of &dhpackage;.
+ <citerefentry>
+ <refentrytitle>primer3_core</refentrytitle>
+ <manvolnum>1</manvolnum>
+ </citerefentry>
+ <citerefentry>
+ <refentrytitle>oligotm</refentrytitle>
+ <manvolnum>1</manvolnum>
+ </citerefentry>
</para>
-
- <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 Primer3 itself.
- </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:
--->
-
-
Modified: trunk/packages/primer3/trunk/debian/oligotm.1.xml
===================================================================
--- trunk/packages/primer3/trunk/debian/oligotm.1.xml 2007-02-17 04:31:55 UTC (rev 211)
+++ trunk/packages/primer3/trunk/debian/oligotm.1.xml 2007-02-17 09:11:56 UTC (rev 212)
@@ -1,14 +1,16 @@
<?xml version='1.0' encoding='ISO-8859-1'?>
<!DOCTYPE refentry PUBLIC "-//OASIS//DTD DocBook XML V4.4//EN"
"/usr/share/xml/docbook/schema/dtd/4.4/docbookx.dtd" [
- <!ENTITY dhfirstname "<firstname>CHARLES</firstname>">
- <!ENTITY dhsurname "<surname>PLESSY</surname>">
- <!ENTITY dhdate "<date>September 28, 2006</date>">
+ <!ENTITY dhfirstname "<firstname>Charles</firstname>">
+ <!ENTITY dhsurname "<surname>Plessy</surname>">
+ <!ENTITY dhdate "<date>February 17, 2007</date>">
<!ENTITY dhsection "<manvolnum>1</manvolnum>">
<!ENTITY dhemail "<email>charles-debian-nospam at plessy.org</email>">
<!ENTITY dhusername "Charles Plessy">
<!ENTITY dhucpackage "<refentrytitle>OLIGOTM</refentrytitle>">
+ <!ENTITY dhtitle "Primer3 User Manuals">
<!ENTITY dhpackage "oligotm">
+ <!ENTITY dhrelease "1.1.0~beta">
<!ENTITY debian "<productname>Debian</productname>">
<!ENTITY gnu "<acronym>GNU</acronym>">
<!ENTITY gpl "&gnu; <acronym>GPL</acronym>">
@@ -16,6 +18,10 @@
<refentry>
<refentryinfo>
+ <title>&dhtitle;</title>
+ <productname>&dhpackage;</productname>
+ <releaseinfo role="version">&dhrelease;</releaseinfo>
+ &dhdate;
<address>
&dhemail;
</address>
@@ -24,62 +30,140 @@
&dhsurname;
</author> -->
<copyright>
- <year>2006</year>
- <holder>&dhusername;</holder>
+ <year>1996,1997,1998,1999,2000,2001,2004,2006</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>
&dhdate;
</refentryinfo>
+
<refmeta>
&dhucpackage;
-
&dhsection;
</refmeta>
+
<refnamediv>
<refname>&dhpackage;</refname>
-
- <refpurpose>Prints oligo's melting temperature on stdout.</refpurpose>
+ <refpurpose>Prints oligo's melting temperature on stdout</refpurpose>
</refnamediv>
+
<refsynopsisdiv>
<cmdsynopsis>
<command>&dhpackage;</command>
- <arg choice="opt">-k <replaceable class="parameter">salt-conc</replaceable></arg>
- <arg choice="opt">-d <replaceable class="parameter">template-conc</replaceable></arg>
- <arg choice="req"><replaceable class="parameter">oligo</replaceable></arg>
+ <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>
+
+ <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 Primer3 package.
+ <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>
+ <refsect1 id="options">
<title>OPTIONS</title>
-
<variablelist>
<varlistentry>
<term>
- <option>-k</option> <parameter>salt-conc</parameter>
+ <option>-mv</option> <parameter>monovalent_conc</parameter>
</term>
<listitem>
- <para><parameter>salt-conc</parameter> is mM salt (usually K) concentration; defaults to 50mM.</para>
+ <para>Concentration of monovalent cations in mM, by default 50 mM.</para>
</listitem>
</varlistentry>
<varlistentry>
<term>
- <option>-t</option> <parameter>template-conc</parameter>
+ <option>-dv</option> <parameter>divalent_conc</parameter>
</term>
<listitem>
- <para><parameter>template-conc</parameter> is nM template concentration; defaults to 50nM.</para>
+ <para>Concentration of divalent cations in mM, by default 0 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 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 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>
+ <refsect1 id="reference">
<title>REFERENCE</title>
<para>
Please cite Rozen, S., Skaletsky, H. "Primer3 on the WWW for general users
@@ -90,46 +174,17 @@
</para>
</refsect1>
- <refsect1>
+ <refsect1 id="see_also">
<title>SEE ALSO</title>
-
- <para>primer3_core (1), ntdpal (1).</para>
-
- </refsect1>
- <refsect1>
- <title>COPYRIGHTS</title>
-
<para>
- Copyright (c) 1996,1997,1998,1999,2000,2001,2004,2006 Steve Rozen, Helen Skaletsky, and Whitehead
- Institute for Biomedical Research. On Debian-based systems, please consult
- <filename>/usr/share/doc/primer3/copyright</filename> to read the licence
- of &dhpackage;.
+ <citerefentry>
+ <refentrytitle>primer3_core</refentrytitle>
+ <manvolnum>1</manvolnum>
+ </citerefentry>
+ <citerefentry>
+ <refentrytitle>ntdpal</refentrytitle>
+ <manvolnum>1</manvolnum>
+ </citerefentry>
</para>
-
- <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 Primer3 itself.<!-- This also applies to this source document -->
- </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:
--->
-
-
Modified: trunk/packages/primer3/trunk/debian/primer3.docs
===================================================================
--- trunk/packages/primer3/trunk/debian/primer3.docs 2007-02-17 04:31:55 UTC (rev 211)
+++ trunk/packages/primer3/trunk/debian/primer3.docs 2007-02-17 09:11:56 UTC (rev 212)
@@ -1,3 +1,3 @@
-README.primer3_1.0b.txt
+README.txt
src/release_notes.txt
how-to-cite.txt
Modified: trunk/packages/primer3/trunk/debian/primer3_core.1.xml
===================================================================
--- trunk/packages/primer3/trunk/debian/primer3_core.1.xml 2007-02-17 04:31:55 UTC (rev 211)
+++ trunk/packages/primer3/trunk/debian/primer3_core.1.xml 2007-02-17 09:11:56 UTC (rev 212)
@@ -3,12 +3,14 @@
<!ENTITY dhfirstname "<firstname>Steffen</firstname>">
<!ENTITY dhsurname "<surname>Moeller</surname>">
<!-- Please adjust the date whenever revising the manpage. -->
- <!ENTITY dhdate "<date>September 13, 2006</date>">
+ <!ENTITY dhdate "<date>February 17, 2007</date>">
+ <!ENTITY dhtitle "Primer3 User Manuals">
<!ENTITY dhsection "<manvolnum>1</manvolnum>">
<!ENTITY dhemail "<email>steffen_moeller at gmx.de</email>">
<!ENTITY dhusername "Steffen Moeller">
<!ENTITY dhucpackage "<refentrytitle>PRIMER3_CORE</refentrytitle>">
<!ENTITY dhpackage "primer3_core">
+ <!ENTITY dhrelease "1.1.0~beta">
<!ENTITY debian "<productname>Debian</productname>">
<!ENTITY gnu "<acronym>GNU</acronym>">
<!ENTITY gpl "&gnu; <acronym>GPL</acronym>">
@@ -16,6 +18,10 @@
<refentry>
<refentryinfo>
+ <title>&dhtitle;</title>
+ <productname>&dhpackage;</productname>
+ <releaseinfo role="version">&dhrelease;</releaseinfo>
+ &dhdate;
<address>
&dhemail;
</address>
@@ -24,10 +30,22 @@
&dhsurname;
</author> -->
<copyright>
- <year>2003, 2006</year>
- <holder>&dhusername;, Charles Plessy</holder>
+ <year>1996,1997,1998,1999,2000,2001,2004,2006</year>
+ <holder>Whitehead Institute for Biomedical Research</holder>
+ <holder>Steve Rozen (http://jura.wi.mit.edu/rozen)</holder>
+ <holder>Helen Skaletsky</holder>
</copyright>
- &dhdate;
+
+ <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;
@@ -43,7 +61,7 @@
<cmdsynopsis>
<command>&dhpackage;</command>
<arg choice="opt">-format_output</arg>
- <arg choice="opt">-2x_compat</arg>
+ <!-- <arg choice="opt">-2x_compat</arg> -->
<arg choice="opt">-strict_tags</arg>
<arg choice="opt">< <replaceable>input_file</replaceable></arg>
</cmdsynopsis>
@@ -72,7 +90,7 @@
<para> Prints a more user-oriented report for each sequence.</para>
</listitem>
</varlistentry>
-
+<!--
<varlistentry>
<term>
<option>-2x_compat</option>
@@ -81,7 +99,7 @@
<para>Print the output using Primer v2 compatible tag names.</para>
</listitem>
</varlistentry>
-
+-->
<varlistentry>
<term>
<option>-strict_tags</option>
@@ -93,6 +111,8 @@
</listitem>
</varlistentry>
</variablelist>
+
+ <note><para>The old flag -2x_compat is no longer supported.</para></note>
</refsect1>
<refsect1>
@@ -115,18 +135,18 @@
<refsect1>
<title>SEE ALSO</title>
- <para>ntdpal (1), oligotm (1).</para>
- </refsect1>
-
- <refsect1>
- <title>COPYRIGHTS</title>
-
<para>
- Copyright (c) 1996,1997,1998,1999,2000,2001,2004,2006 Steve Rozen, Helen Skaletsky, and Whitehead Institute for Biomedical Research. On Debian-based systems, please consult <filename>/usr/share/doc/primer3/copyright</filename> to read the licence of &dhpackage;.
+ <citerefentry>
+ <refentrytitle>ntdpal</refentrytitle>
+ <manvolnum>1</manvolnum>
+ </citerefentry>
+
+ <citerefentry>
+ <refentrytitle>oligotm</refentrytitle>
+ <manvolnum>1</manvolnum>
+ </citerefentry>
</para>
+ </refsect1>
- <para>This manual page was written by &dhusername; &dhemail; and Charles Plessy 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 Primer3 itself.
- </para>
- </refsect1>
</refentry>
Modified: trunk/packages/primer3/trunk/debian/rules
===================================================================
--- trunk/packages/primer3/trunk/debian/rules 2007-02-17 04:31:55 UTC (rev 211)
+++ trunk/packages/primer3/trunk/debian/rules 2007-02-17 09:11:56 UTC (rev 212)
@@ -18,11 +18,8 @@
endif
DEB_HOST_ARCH_CPU ?= $(shell dpkg-architecture -qDEB_HOST_ARCH_CPU)
-
-SKIP_TEST_CPUS := arm m68k s390
-
+SKIP_TEST_CPUS := arm m68k s390 powerpc
PRIMER_EXE = primer3_core
-
EXES=$(PRIMER_EXE) ntdpal oligotm long_seq_tm_test
build: manpages
@@ -36,23 +33,23 @@
tests: build-stamp tests-clean
ifeq (,$(filter $(DEB_HOST_ARCH_CPU),$(SKIP_TEST_CPUS)))
- cp -al test tests
- cd tests ; cow-shell perl p3test.pl ; cow-shell perl dpal_test.pl
+ $(MAKE) -C test test
else
@echo "Slow-cpu arch detected, skipping test"
endif
touch tests-stamp
tests-clean:
- rm -rf tests tests-stamp
+ $(MAKE) -C test clean
clean: tests-clean
dh_testdir
dh_testroot
rm -f build-stamp
+ $(MAKE) -C src clean
# make clean fails on clean sources, so I clean with this:
- cd src ; rm -f *.o $(EXES) *~
+ # cd src ; rm -f *.o $(EXES) *~
dh_clean debian/primer3_core.1 debian/ntdpal.1 debian/oligotm.1 debian/manpages
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