[med-svn] r403 - trunk/packages/muscle/trunk/debian
charles-guest at alioth.debian.org
charles-guest at alioth.debian.org
Tue Aug 14 03:01:33 UTC 2007
Author: charles-guest
Date: 2007-08-14 03:01:33 +0000 (Tue, 14 Aug 2007)
New Revision: 403
Modified:
trunk/packages/muscle/trunk/debian/changelog
trunk/packages/muscle/trunk/debian/manpage.xml
trunk/packages/muscle/trunk/debian/rules
Log:
Updating manpage
Modified: trunk/packages/muscle/trunk/debian/changelog
===================================================================
--- trunk/packages/muscle/trunk/debian/changelog 2007-08-14 01:55:23 UTC (rev 402)
+++ trunk/packages/muscle/trunk/debian/changelog 2007-08-14 03:01:33 UTC (rev 403)
@@ -4,8 +4,9 @@
* Enhaces: seaview because SeaView can call muscle to re-align sequences.
* Handling nostrip build option (policy 10.1) (Closes: #437599).
* Updating Steffen's email adress.
+ * Updating manpage.
- -- Charles Plessy <charles-debian-nospam at plessy.org> Tue, 14 Aug 2007 10:51:05 +0900
+ -- Charles Plessy <charles-debian-nospam at plessy.org> Tue, 14 Aug 2007 12:01:07 +0900
muscle (3.60-1) unstable; urgency=low
Modified: trunk/packages/muscle/trunk/debian/manpage.xml
===================================================================
--- trunk/packages/muscle/trunk/debian/manpage.xml 2007-08-14 01:55:23 UTC (rev 402)
+++ trunk/packages/muscle/trunk/debian/manpage.xml 2007-08-14 03:01:33 UTC (rev 403)
@@ -1,6 +1,8 @@
-<?xml version='1.0' encoding='ISO-8859-1'?>
-<!DOCTYPE refentry PUBLIC "-//OASIS//DTD DocBook XML V4.2//EN"
-"http://www.oasis-open.org/docbook/xml/4.2/docbookx.dtd" [
+<?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 V4.4//EN"
+ "http://www.oasis-open.org/docbook/xml/4.4/docbookx.dtd" [
<!--
@@ -26,68 +28,97 @@
-->
- <!-- Fill in your name for FIRSTNAME and SURNAME. -->
- <!ENTITY dhfirstname "<firstname>Steffen</firstname>">
- <!ENTITY dhsurname "<surname>Moeller</surname>">
- <!-- Please adjust the date whenever revising the manpage. -->
- <!ENTITY dhdate "<date>September 19, 2004</date>">
- <!-- SECTION should be 1-8, maybe w/ subsection other parameters are
- allowed: see man(7), man(1). -->
+ <!ENTITY dhfirstname "Steffen">
+ <!ENTITY dhsurname "Moeller">
<!ENTITY dhsection "<manvolnum>1</manvolnum>">
- <!ENTITY dhemail "<email>moeller at debian.org</email>">
+ <!ENTITY dhemail "moeller at debian.org">
<!ENTITY dhusername "Steffen Moeller">
<!ENTITY dhucpackage "<refentrytitle>MUSCLE</refentrytitle>">
<!ENTITY dhpackage "muscle">
-
<!ENTITY debian "<productname>Debian</productname>">
<!ENTITY gnu "<acronym>GNU</acronym>">
<!ENTITY gpl "&gnu; <acronym>GPL</acronym>">
+ <!ENTITY dhrelease "3.6">
+ <!ENTITY dhtitle "Muscle Manual">
]>
<refentry>
<refentryinfo>
- <address>
- &dhemail;
- </address>
- <author>
- &dhfirstname;
- &dhsurname;
- </author>
+ <title>&dhtitle;</title>
+ <productname>&dhpackage;</productname>
+ <releaseinfo role="version">&dhrelease;</releaseinfo>
+ <authorgroup>
+ <author>
+ <firstname>Robert</firstname>
+ <firstname>C.</firstname>
+ <surname>Elgar</surname>
+ <contrib>Wrote Muscle.</contrib>
+ </author>
+ <author>
+ <firstname>&dhfirstname;</firstname>
+ <surname>&dhsurname;</surname>
+ <contrib>Wrote this manpage.</contrib>
+ <address><email>&dhemail;</email></address>
+ </author>
+ <author>
+ <firstname>Charles</firstname>
+ <surname>Plessy</surname>
+ <contrib>Updated this manpage.</contrib>
+ <address><email>charles-debian-nospam at plessy.org</email></address>
+ </author>
+ </authorgroup>
<copyright>
<year>2003</year>
- <holder>&dhusername;</holder>
+ <year>2004</year>
+ <holder>&dhusername; (manpage)</holder>
</copyright>
- &dhdate;
+ <copyright>
+ <year>2007</year>
+ <holder>Charles Plessy (manpage)</holder>
+ </copyright>
+ <legalnotice>
+ <para>
+ Muscle is in the public domain, and therefore not subjected to copyright.
+ </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 as if it were in public domain.
+ </para>
+ </legalnotice>
</refentryinfo>
+
<refmeta>
&dhucpackage;
-
&dhsection;
</refmeta>
+
<refnamediv>
<refname>&dhpackage;</refname>
-
<refpurpose>Multiple Protein Sequence Alignment</refpurpose>
</refnamediv>
+
<refsynopsisdiv>
<cmdsynopsis>
<command>&dhpackage;</command>
- <arg><option>-in <replaceable>input file (fasta)</replaceable></option></arg>
- <arg><option>-out <replaceable>output file (default fasta)</replaceable></option></arg>
- <arg><option>-log <replaceable>log file</replaceable></option></arg>
- <arg><option>-maxiters <replaceable>n</replaceable></option></arg>
- <arg><option>-maxhours <replaceable>n</replaceable></option></arg>
- <arg><option>-clw</option></arg>
- <arg><option>-clwstrict</option></arg>
- <arg><option>-html</option></arg>
- <arg><option>-msf</option></arg>
- <arg><option>-quiet</option></arg>
- <arg><option>-group</option></arg>
- <arg><option>-stable</option></arg>
- <arg><option>-version</option></arg>
- <arg><option>-out <replaceable>output file</replaceable></option></arg>
+ <arg choice="plain"><option>-in <replaceable>input file (fasta)</replaceable></option></arg>
+ <arg choice="opt"><option>-out <replaceable>output file (default fasta)</replaceable></option></arg>
+ <arg choice="opt"><option>-diags</option></arg>
+ <arg choice="opt"><option>-log <replaceable>log file</replaceable></option></arg>
+ <arg choice="opt"><option>-maxiters <replaceable>n</replaceable></option></arg>
+ <arg choice="opt"><option>-maxhours <replaceable>n</replaceable></option></arg>
+ <arg choice="opt"><option>-maxmb <replaceable>m</replaceable></option></arg>
+ <arg choice="opt"><option>-html</option></arg>
+ <arg choice="opt"><option>-msf</option></arg>
+ <arg choice="opt"><option>-clw</option></arg>
+ <arg choice="opt"><option>-clwstrict</option></arg>
+ <arg choice="opt"><option>-log[a] <replaceable>logfile</replaceable></option></arg>
+ <arg choice="opt"><option>-quiet</option></arg>
+ <arg choice="opt"><option>-stable</option></arg>
+ <arg choice="opt"><option>-group</option></arg>
+ <arg choice="opt"><option>-version</option></arg>
</cmdsynopsis>
</refsynopsisdiv>
+
<refsect1>
<title>DESCRIPTION</title>
@@ -95,13 +126,9 @@
<command>&dhpackage;</command> command.
</para>
- <para>This manual page was written for the &debian; distribution
- because the original program does not have a manual page.
- </para>
-
<para><command>&dhpackage;</command> aligns protein sequences and is considered superior and faster than clustalw.</para>
-
</refsect1>
+
<refsect1>
<title>OPTIONS</title>
<variablelist>
@@ -137,34 +164,44 @@
</para>
</listitem>
</varlistentry>
+
<varlistentry>
- <term><option>-clw</option>
+ <term><option>-maxmb <replaceable>m</replaceable></option></term>
+ <listitem>
+ <para>Maximum memory to allocate in Mb (default 80% of RAM)</para>
+ </listitem>
+ </varlistentry>
+
+ <varlistentry>
+ <term><option>-html</option>
</term>
<listitem>
- <para>Write output in CLUSTALW format (default FASTA)</para>
+ <para>Write output in HTML format (default FASTA)</para>
</listitem>
</varlistentry>
<varlistentry>
- <term><option>-clwstrict</option>
+ <term><option>-msf</option>
</term>
<listitem>
- <para>As -clw, with 'CLUSTAL W (1.81)' header</para>
+ <para>Write output in MSF format (default FASTA)</para>
</listitem>
</varlistentry>
+
<varlistentry>
- <term><option>-html</option>
+ <term><option>-clw</option>
</term>
<listitem>
- <para>Write output in HTML format (default FASTA)</para>
+ <para>Write output in CLUSTALW format (default FASTA)</para>
</listitem>
</varlistentry>
<varlistentry>
- <term><option>-msf</option>
+ <term><option>-clwstrict</option>
</term>
<listitem>
- <para>Write output in MSF format (default FASTA)</para>
+ <para>As -clw, with 'CLUSTAL W (1.81)' header</para>
</listitem>
</varlistentry>
+
<varlistentry>
<term><option>-log[a] <replaceable>logfile</replaceable></option>
</term>
@@ -204,20 +241,16 @@
</refsect1>
<refsect1>
<title>SEE ALSO</title>
- <para>clustalw (1), seaview (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>
+ <citerefentry>
+ <refentrytitle>clustalw</refentrytitle>
+ <manvolnum>1</manvolnum>
+ </citerefentry>,
+
+ <citerefentry>
+ <refentrytitle>seaview</refentrytitle>
+ <manvolnum>1</manvolnum>
+ </citerefentry>.
</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>
-
Modified: trunk/packages/muscle/trunk/debian/rules
===================================================================
--- trunk/packages/muscle/trunk/debian/rules 2007-08-14 01:55:23 UTC (rev 402)
+++ trunk/packages/muscle/trunk/debian/rules 2007-08-14 03:01:33 UTC (rev 403)
@@ -38,7 +38,7 @@
# Add here commands to compile the package.
$(MAKE) CFLAGS="$(CFLAGS)"
#/usr/bin/docbook-to-man debian/muscle.sgml > muscle.1
- xsltproc -''-nonet /usr/share/sgml/docbook/stylesheet/xsl/nwalsh/manpages/docbook.xsl debian/manpage.xml
+ xsltproc --nonet debian/manpage.xml
touch build-stamp
clean:
More information about the debian-med-commit
mailing list