[med-svn] r99 - in trunk/packages/primer3/trunk: . debian
Charles Plessy
charles-guest at costa.debian.org
Mon Aug 28 15:01:04 UTC 2006
Author: charles-guest
Date: 2006-08-28 15:01:02 +0000 (Mon, 28 Aug 2006)
New Revision: 99
Added:
trunk/packages/primer3/trunk/debian/ntdpal.1.xml
trunk/packages/primer3/trunk/debian/primer3.dirs
trunk/packages/primer3/trunk/debian/primer3.docs
trunk/packages/primer3/trunk/debian/primer3.install
trunk/packages/primer3/trunk/debian/primer3.manpages
trunk/packages/primer3/trunk/debian/primer3.sgml
Removed:
trunk/packages/primer3/trunk/debian/dirs
trunk/packages/primer3/trunk/debian/docs
trunk/packages/primer3/trunk/debian/install
trunk/packages/primer3/trunk/debian/manpages
trunk/packages/primer3/trunk/primer3.sgml
Modified:
trunk/packages/primer3/trunk/debian/rules
Log:
Adding ntdpal to the primer3 package
Deleted: trunk/packages/primer3/trunk/debian/dirs
===================================================================
--- trunk/packages/primer3/trunk/debian/dirs 2006-08-23 14:53:19 UTC (rev 98)
+++ trunk/packages/primer3/trunk/debian/dirs 2006-08-28 15:01:02 UTC (rev 99)
@@ -1,3 +0,0 @@
-usr/bin
-usr/lib/cgi-bin
-var/www
Deleted: trunk/packages/primer3/trunk/debian/docs
===================================================================
--- trunk/packages/primer3/trunk/debian/docs 2006-08-23 14:53:19 UTC (rev 98)
+++ trunk/packages/primer3/trunk/debian/docs 2006-08-28 15:01:02 UTC (rev 99)
@@ -1,2 +0,0 @@
-README
-src/release_notes
Deleted: trunk/packages/primer3/trunk/debian/install
===================================================================
--- trunk/packages/primer3/trunk/debian/install 2006-08-23 14:53:19 UTC (rev 98)
+++ trunk/packages/primer3/trunk/debian/install 2006-08-28 15:01:02 UTC (rev 99)
@@ -1,4 +0,0 @@
-src/primer3_core usr/bin
-#src/primer*www*.html var/www
-#src/primer*www*.cgi usr/lib/cgi-bin
-
Deleted: trunk/packages/primer3/trunk/debian/manpages
===================================================================
--- trunk/packages/primer3/trunk/debian/manpages 2006-08-23 14:53:19 UTC (rev 98)
+++ trunk/packages/primer3/trunk/debian/manpages 2006-08-28 15:01:02 UTC (rev 99)
@@ -1 +0,0 @@
-primer3.1
Added: trunk/packages/primer3/trunk/debian/ntdpal.1.xml
===================================================================
--- trunk/packages/primer3/trunk/debian/ntdpal.1.xml 2006-08-23 14:53:19 UTC (rev 98)
+++ trunk/packages/primer3/trunk/debian/ntdpal.1.xml 2006-08-28 15:01:02 UTC (rev 99)
@@ -0,0 +1,242 @@
+<?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 dhsection "<manvolnum>1</manvolnum>">
+ <!ENTITY dhemail "<email>charles-debian-nospam at plessy.org</email>">
+ <!ENTITY dhusername "Charles Plessy">
+ <!ENTITY dhucpackage "<refentrytitle>NTDPAL</refentrytitle>">
+ <!ENTITY dhpackage "ntdpal">
+ <!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>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">-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>
+ </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>primer3_core (1)</para>
+
+ </refsect1>
+ <refsect1>
+ <title>COPYRIGHTS</title>
+
+ <para>
+ Copyright (c) 1996, 2002, 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;.
+ </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 &dhpackage; 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:
+-->
+
+
Added: trunk/packages/primer3/trunk/debian/primer3.dirs
===================================================================
--- trunk/packages/primer3/trunk/debian/primer3.dirs 2006-08-23 14:53:19 UTC (rev 98)
+++ trunk/packages/primer3/trunk/debian/primer3.dirs 2006-08-28 15:01:02 UTC (rev 99)
@@ -0,0 +1,3 @@
+usr/bin
+usr/lib/cgi-bin
+var/www
Added: trunk/packages/primer3/trunk/debian/primer3.docs
===================================================================
--- trunk/packages/primer3/trunk/debian/primer3.docs 2006-08-23 14:53:19 UTC (rev 98)
+++ trunk/packages/primer3/trunk/debian/primer3.docs 2006-08-28 15:01:02 UTC (rev 99)
@@ -0,0 +1,2 @@
+README
+src/release_notes
Added: trunk/packages/primer3/trunk/debian/primer3.install
===================================================================
--- trunk/packages/primer3/trunk/debian/primer3.install 2006-08-23 14:53:19 UTC (rev 98)
+++ trunk/packages/primer3/trunk/debian/primer3.install 2006-08-28 15:01:02 UTC (rev 99)
@@ -0,0 +1,5 @@
+src/primer3_core usr/bin
+src/ntdpal usr/bin
+#src/primer*www*.html var/www
+#src/primer*www*.cgi usr/lib/cgi-bin
+
Added: trunk/packages/primer3/trunk/debian/primer3.manpages
===================================================================
--- trunk/packages/primer3/trunk/debian/primer3.manpages 2006-08-23 14:53:19 UTC (rev 98)
+++ trunk/packages/primer3/trunk/debian/primer3.manpages 2006-08-28 15:01:02 UTC (rev 99)
@@ -0,0 +1,2 @@
+debian/ntdpal
+debian/primer3.1
Added: trunk/packages/primer3/trunk/debian/primer3.sgml
===================================================================
--- trunk/packages/primer3/trunk/debian/primer3.sgml 2006-08-23 14:53:19 UTC (rev 98)
+++ trunk/packages/primer3/trunk/debian/primer3.sgml 2006-08-28 15:01:02 UTC (rev 99)
@@ -0,0 +1,115 @@
+<!doctype refentry PUBLIC "-//OASIS//DTD DocBook V4.1//EN" [
+
+ <!-- Fill in your name for FIRSTNAME and SURNAME. -->
+ <!ENTITY dhfirstname "<firstname>FIRSTNAME</firstname>">
+ <!ENTITY dhsurname "<surname>SURNAME</surname>">
+ <!-- Please adjust the date whenever revising the manpage. -->
+ <!ENTITY dhdate "<date>March 31, 2004</date>">
+ <!-- SECTION should be 1-8, maybe w/ subsection other parameters are
+ allowed: see man(7), man(1). -->
+ <!ENTITY dhsection "<manvolnum>SECTION</manvolnum>">
+ <!ENTITY dhemail "<email>moeller at pzr.uni-rostock.de</email>">
+ <!ENTITY dhusername "Steffen Moeller">
+ <!ENTITY dhucpackage "<refentrytitle>PRIMER3</refentrytitle>">
+ <!ENTITY dhpackage "primer3">
+
+ <!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>2003</year>
+ <holder>&dhusername;</holder>
+ </copyright>
+ &dhdate;
+ </refentryinfo>
+ <refmeta>
+ &dhucpackage;
+
+ &dhsection;
+ </refmeta>
+ <refnamediv>
+ <refname>&dhpackage;</refname>
+
+ <refpurpose>Designs primers for PCR</refpurpose>
+ </refnamediv>
+ <refsynopsisdiv>
+ <cmdsynopsis>
+ <command>&dhpackage;_core</command>
+ </cmdsynopsis>
+ </refsynopsisdiv>
+ <refsect1>
+ <title>DESCRIPTION</title>
+
+ <para>This manual page was written for the &debian; distribution
+ because the original program does not have a manual page.
+ </para>
+ <para>
+Primer3 determines oligos for the polymerase chain reaction (PCR) to create copies of a DNA sequence.
+Constrains on the oligos, like their minimal, desired and maximal length, melting temperature and many other criteria may be specified.
+ </para>
+ <para>
+The package installs a CGI script for the package in /usr/lib/cgi-bin with its help files in /var/www which works for single sequences. The package itself may be used for batch queries and is not interactive. It expects sequences to be piped in via stdin in a format descripted in detail in the README file. The web interface and its introduction is a good introduction, too.
+ </para>
+ <para>
+ The program was created by Steve Rozen and Helen J. Skaletsky (1996,1997,1998).
+ </para>
+
+ </refsect1>
+ <refsect1>
+ <title>SEE ALSO</title>
+
+ <para>e-PCR (of the ncbi-epcr package) (1)</para>
+
+ <para>http://localhost/cgi-bin/primer3_www.cgi</para>
+
+ <para>The program is well described by the
+ <citetitle>README</citetitle> file available
+ in /usr/share/doc/primer3.
+ </para>
+ <para>http://www-genome.wi.mit.edu/genome_software/other/primer3.html</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:
+-->
+
+
Modified: trunk/packages/primer3/trunk/debian/rules
===================================================================
--- trunk/packages/primer3/trunk/debian/rules 2006-08-23 14:53:19 UTC (rev 98)
+++ trunk/packages/primer3/trunk/debian/rules 2006-08-28 15:01:02 UTC (rev 99)
@@ -23,7 +23,7 @@
dh_testdir
# Add here commands to compile the package.
- $(MAKE) -C src
+ $(MAKE) -C src all ntdpal
touch build-stamp
clean:
@@ -34,12 +34,18 @@
# Add here commands to clean up after the build process.
-$(MAKE) -C src clean
- dh_clean primer3_core.1 primer3.1
+ dh_clean debian/primer3.1 debian/ntdpal.1 debian/manpages
-primer3.1: primer3.sgml
+debian/primer3.1: debian/primer3.sgml
docbook-to-man $< > $@
-install: build primer3.1
+debian/ntdpal.1: debian/ntdpal.1.xml
+ xsltproc -o debian/ -''-nonet /usr/share/xml/docbook/stylesheet/nwalsh/manpages/docbook.xsl $<
+
+manpages: debian/primer3.1 debian/ntdpal.1
+ touch debian/manpages
+
+install: build manpages
dh_testdir
dh_testroot
dh_clean -k
Deleted: trunk/packages/primer3/trunk/primer3.sgml
===================================================================
--- trunk/packages/primer3/trunk/primer3.sgml 2006-08-23 14:53:19 UTC (rev 98)
+++ trunk/packages/primer3/trunk/primer3.sgml 2006-08-28 15:01:02 UTC (rev 99)
@@ -1,115 +0,0 @@
-<!doctype refentry PUBLIC "-//OASIS//DTD DocBook V4.1//EN" [
-
- <!-- Fill in your name for FIRSTNAME and SURNAME. -->
- <!ENTITY dhfirstname "<firstname>FIRSTNAME</firstname>">
- <!ENTITY dhsurname "<surname>SURNAME</surname>">
- <!-- Please adjust the date whenever revising the manpage. -->
- <!ENTITY dhdate "<date>March 31, 2004</date>">
- <!-- SECTION should be 1-8, maybe w/ subsection other parameters are
- allowed: see man(7), man(1). -->
- <!ENTITY dhsection "<manvolnum>SECTION</manvolnum>">
- <!ENTITY dhemail "<email>moeller at pzr.uni-rostock.de</email>">
- <!ENTITY dhusername "Steffen Moeller">
- <!ENTITY dhucpackage "<refentrytitle>PRIMER3</refentrytitle>">
- <!ENTITY dhpackage "primer3">
-
- <!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>2003</year>
- <holder>&dhusername;</holder>
- </copyright>
- &dhdate;
- </refentryinfo>
- <refmeta>
- &dhucpackage;
-
- &dhsection;
- </refmeta>
- <refnamediv>
- <refname>&dhpackage;</refname>
-
- <refpurpose>Designs primers for PCR</refpurpose>
- </refnamediv>
- <refsynopsisdiv>
- <cmdsynopsis>
- <command>&dhpackage;_core</command>
- </cmdsynopsis>
- </refsynopsisdiv>
- <refsect1>
- <title>DESCRIPTION</title>
-
- <para>This manual page was written for the &debian; distribution
- because the original program does not have a manual page.
- </para>
- <para>
-Primer3 determines oligos for the polymerase chain reaction (PCR) to create copies of a DNA sequence.
-Constrains on the oligos, like their minimal, desired and maximal length, melting temperature and many other criteria may be specified.
- </para>
- <para>
-The package installs a CGI script for the package in /usr/lib/cgi-bin with its help files in /var/www which works for single sequences. The package itself may be used for batch queries and is not interactive. It expects sequences to be piped in via stdin in a format descripted in detail in the README file. The web interface and its introduction is a good introduction, too.
- </para>
- <para>
- The program was created by Steve Rozen and Helen J. Skaletsky (1996,1997,1998).
- </para>
-
- </refsect1>
- <refsect1>
- <title>SEE ALSO</title>
-
- <para>e-PCR (of the ncbi-epcr package) (1)</para>
-
- <para>http://localhost/cgi-bin/primer3_www.cgi</para>
-
- <para>The program is well described by the
- <citetitle>README</citetitle> file available
- in /usr/share/doc/primer3.
- </para>
- <para>http://www-genome.wi.mit.edu/genome_software/other/primer3.html</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:
--->
-
-
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