[med-svn] r832 - trunk/packages/muscle/trunk/debian
hanska-guest at alioth.debian.org
hanska-guest at alioth.debian.org
Sun Nov 18 10:37:03 UTC 2007
Author: hanska-guest
Date: 2007-11-18 10:37:03 +0000 (Sun, 18 Nov 2007)
New Revision: 832
Added:
trunk/packages/muscle/trunk/debian/muscle.1
trunk/packages/muscle/trunk/debian/muscle.1.xml
Removed:
trunk/packages/muscle/trunk/debian/manpage.xml
trunk/packages/muscle/trunk/debian/manpages
Modified:
trunk/packages/muscle/trunk/debian/changelog
trunk/packages/muscle/trunk/debian/control
trunk/packages/muscle/trunk/debian/rules
Log:
* debian/manpage.xml moved to debian/muscle.1.xml
* debian/muscle.1 added - statically built
* debian/manpages removed - passing arguments to dh_installman
directly
* debian/control:
- B-D updated (see above)
- added myself to Uploaders
- moved XS-Vcs-* to Vcs-*
* debian/rules:
- manpages statically built
- minor changes
Modified: trunk/packages/muscle/trunk/debian/changelog
===================================================================
--- trunk/packages/muscle/trunk/debian/changelog 2007-11-18 10:23:35 UTC (rev 831)
+++ trunk/packages/muscle/trunk/debian/changelog 2007-11-18 10:37:03 UTC (rev 832)
@@ -13,8 +13,21 @@
[ Nelson A. de Oliveira ]
* Added watch file.
- -- Charles Plessy <charles-debian-nospam at plessy.org> Fri, 21 Sep 2007 23:08:06 +0900
+ [ David Paleino ]
+ * debian/manpage.xml moved to debian/muscle.1.xml
+ * debian/muscle.1 added - statically built
+ * debian/manpages removed - passing arguments to dh_installman
+ directly
+ * debian/control:
+ - B-D updated (see above)
+ - added myself to Uploaders
+ - moved XS-Vcs-* to Vcs-*
+ * debian/rules:
+ - manpages statically built
+ - minor changes
+ -- David Paleino <d.paleino at gmail.com> Sun, 18 Nov 2007 11:34:11 +0100
+
muscle (3.60-1) unstable; urgency=low
* New upstram release (Closes: Bug#361742).
Modified: trunk/packages/muscle/trunk/debian/control
===================================================================
--- trunk/packages/muscle/trunk/debian/control 2007-11-18 10:23:35 UTC (rev 831)
+++ trunk/packages/muscle/trunk/debian/control 2007-11-18 10:37:03 UTC (rev 832)
@@ -2,11 +2,13 @@
Section: science
Priority: optional
Maintainer: Debian-Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
-Uploaders: Steffen Moeller <moeller at debian.org>, Charles Plessy <charles-debian-nospam at plessy.org>
-Build-Depends: debhelper (>= 5.0.0), xsltproc, docbook-xsl, docbook-xml
+Uploaders: Steffen Moeller <moeller at debian.org>,
+ Charles Plessy <charles-debian-nospam at plessy.org>,
+ David Paleino <d.paleino at gmail.com>
+Build-Depends: debhelper (>= 5.0.0)
Standards-Version: 3.7.2
-XS-Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/muscle/trunk/
-XS-Vcs-Svn: svn://svn.debian.org/svn/debian-med/trunk/packages/muscle
+Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/muscle/trunk/
+Vcs-Svn: svn://svn.debian.org/svn/debian-med/trunk/packages/muscle
Homepage: http://www.drive5.com/muscle/
Package: muscle
Deleted: trunk/packages/muscle/trunk/debian/manpage.xml
===================================================================
--- trunk/packages/muscle/trunk/debian/manpage.xml 2007-11-18 10:23:35 UTC (rev 831)
+++ trunk/packages/muscle/trunk/debian/manpage.xml 2007-11-18 10:37:03 UTC (rev 832)
@@ -1,256 +0,0 @@
-<?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" [
-
-<!--
-
-Process this file with an XSLT processor: `xsltproc \
--''-nonet /usr/share/sgml/docbook/stylesheet/xsl/nwalsh/\
-manpages/docbook.xsl manpage.dbk'. A manual page
-<package>.<section> will be generated. You may view the
-manual page with: nroff -man <package>.<section> | less'. A
-typical entry in a Makefile or Makefile.am is:
-
-DB2MAN=/usr/share/sgml/docbook/stylesheet/xsl/nwalsh/\
-manpages/docbook.xsl
-XP=xsltproc -''-nonet
-
-manpage.1: manpage.dbk
- $(XP) $(DB2MAN) $<
-
-The xsltproc binary is found in the xsltproc package. The
-XSL files are in docbook-xsl. Please remember that if you
-create the nroff version in one of the debian/rules file
-targets (such as build), you will need to include xsltproc
-and docbook-xsl in your Build-Depends control field.
-
--->
-
- <!ENTITY dhfirstname "Steffen">
- <!ENTITY dhsurname "Moeller">
- <!ENTITY dhsection "<manvolnum>1</manvolnum>">
- <!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>
- <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>
- <year>2004</year>
- <holder>&dhusername; (manpage)</holder>
- </copyright>
- <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 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>
-
- <para>This manual page documents briefly the
- <command>&dhpackage;</command> command.
- </para>
-
- <para><command>&dhpackage;</command> aligns protein sequences and is considered superior and faster than clustalw.</para>
- </refsect1>
-
- <refsect1>
- <title>OPTIONS</title>
- <variablelist>
- <varlistentry>
- <term><option>-in <replaceable>input file</replaceable></option>
- </term>
- <listitem>
- <para>Path to FASTA formatted input file
- </para>
- </listitem>
- </varlistentry>
- <varlistentry>
- <term><option>-out <replaceable>output file</replaceable></option>
- </term>
- <listitem>
- <para>Path to output file, FASTA formatted by default.
- </para>
- </listitem>
- </varlistentry>
- <varlistentry>
- <term><option>-maxiters <replaceable>n</replaceable></option>
- </term>
- <listitem>
- <para>Maximum number of iterations (integer, default 16)
- </para>
- </listitem>
- </varlistentry>
- <varlistentry>
- <term><option>-maxhours <replaceable>n</replaceable></option>
- </term>
- <listitem>
- <para>Maximum time to iterate in hours (default no limit)
- </para>
- </listitem>
- </varlistentry>
-
- <varlistentry>
- <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 HTML format (default FASTA)</para>
- </listitem>
- </varlistentry>
- <varlistentry>
- <term><option>-msf</option>
- </term>
- <listitem>
- <para>Write output in MSF format (default FASTA)</para>
- </listitem>
- </varlistentry>
-
- <varlistentry>
- <term><option>-clw</option>
- </term>
- <listitem>
- <para>Write output in CLUSTALW format (default FASTA)</para>
- </listitem>
- </varlistentry>
- <varlistentry>
- <term><option>-clwstrict</option>
- </term>
- <listitem>
- <para>As -clw, with 'CLUSTAL W (1.81)' header</para>
- </listitem>
- </varlistentry>
-
- <varlistentry>
- <term><option>-log[a] <replaceable>logfile</replaceable></option>
- </term>
- <listitem>
- <para>Log to file (append if -loga, overwrite if -log)</para>
- </listitem>
- </varlistentry>
- <varlistentry>
- <term><option>-quiet</option>
- </term>
- <listitem>
- <para>Do not write progress messages to stderr</para>
- </listitem>
- </varlistentry>
- <varlistentry>
- <term><option>-stable</option>
- </term>
- <listitem>
- <para>Output sequences in input order (default is -group)</para>
- </listitem>
- </varlistentry>
- <varlistentry>
- <term><option>-group</option>
- </term>
- <listitem>
- <para>Group sequences by similarity (this is the default)</para>
- </listitem>
- </varlistentry>
- <varlistentry>
- <term><option>-version</option>
- </term>
- <listitem>
- <para>Display version information and exit</para>
- </listitem>
- </varlistentry>
- </variablelist>
- </refsect1>
- <refsect1>
- <title>SEE ALSO</title>
- <para>
- <citerefentry>
- <refentrytitle>clustalw</refentrytitle>
- <manvolnum>1</manvolnum>
- </citerefentry>,
-
- <citerefentry>
- <refentrytitle>seaview</refentrytitle>
- <manvolnum>1</manvolnum>
- </citerefentry>.
- </para>
- </refsect1>
-</refentry>
Deleted: trunk/packages/muscle/trunk/debian/manpages
===================================================================
--- trunk/packages/muscle/trunk/debian/manpages 2007-11-18 10:23:35 UTC (rev 831)
+++ trunk/packages/muscle/trunk/debian/manpages 2007-11-18 10:37:03 UTC (rev 832)
@@ -1 +0,0 @@
-muscle.1
Added: trunk/packages/muscle/trunk/debian/muscle.1
===================================================================
--- trunk/packages/muscle/trunk/debian/muscle.1 (rev 0)
+++ trunk/packages/muscle/trunk/debian/muscle.1 2007-11-18 10:37:03 UTC (rev 832)
@@ -0,0 +1,129 @@
+.\" Title: MUSCLE
+.\" Author: Robert Elgar
+.\" Generator: DocBook XSL Stylesheets v1.73.2 <http://docbook.sf.net/>
+.\" Date: 11/18/2007
+.\" Manual: Muscle Manual
+.\" Source: muscle 3.6
+.\"
+.TH "MUSCLE" "1" "11/18/2007" "muscle 3.6" "Muscle Manual"
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.SH "NAME"
+muscle - Multiple Protein Sequence Alignment
+.SH "SYNOPSIS"
+.HP 7
+\fBmuscle\fR \fB\-in\ \fR\fB\fIinput\ file\ (fasta)\fR\fR [\fB\-out\ \fR\fB\fIoutput\ file\ (default\ fasta)\fR\fR] [\fB\-diags\fR] [\fB\-log\ \fR\fB\fIlog\ file\fR\fR] [\fB\-maxiters\ \fR\fB\fIn\fR\fR] [\fB\-maxhours\ \fR\fB\fIn\fR\fR] [\fB\-maxmb\ \fR\fB\fIm\fR\fR] [\fB\-html\fR] [\fB\-msf\fR] [\fB\-clw\fR] [\fB\-clwstrict\fR] [\fB\-log[a]\ \fR\fB\fIlogfile\fR\fR] [\fB\-quiet\fR] [\fB\-stable\fR] [\fB\-group\fR] [\fB\-version\fR]
+.SH "DESCRIPTION"
+.PP
+This manual page documents briefly the
+\fBmuscle\fR
+command\.
+.PP
+\fBmuscle\fR
+aligns protein sequences and is considered superior and faster than clustalw\.
+.SH "OPTIONS"
+.PP
+\fB\-in \fR\fB\fIinput file\fR\fR
+.RS 4
+Path to FASTA formatted input file
+.RE
+.PP
+\fB\-out \fR\fB\fIoutput file\fR\fR
+.RS 4
+Path to output file, FASTA formatted by default\.
+.RE
+.PP
+\fB\-maxiters \fR\fB\fIn\fR\fR
+.RS 4
+Maximum number of iterations (integer, default 16)
+.RE
+.PP
+\fB\-maxhours \fR\fB\fIn\fR\fR
+.RS 4
+Maximum time to iterate in hours (default no limit)
+.RE
+.PP
+\fB\-maxmb \fR\fB\fIm\fR\fR
+.RS 4
+Maximum memory to allocate in Mb (default 80% of RAM)
+.RE
+.PP
+\fB\-html\fR
+.RS 4
+Write output in HTML format (default FASTA)
+.RE
+.PP
+\fB\-msf\fR
+.RS 4
+Write output in MSF format (default FASTA)
+.RE
+.PP
+\fB\-clw\fR
+.RS 4
+Write output in CLUSTALW format (default FASTA)
+.RE
+.PP
+\fB\-clwstrict\fR
+.RS 4
+As \-clw, with \'CLUSTAL W (1\.81)\' header
+.RE
+.PP
+\fB\-log[a] \fR\fB\fIlogfile\fR\fR
+.RS 4
+Log to file (append if \-loga, overwrite if \-log)
+.RE
+.PP
+\fB\-quiet\fR
+.RS 4
+Do not write progress messages to stderr
+.RE
+.PP
+\fB\-stable\fR
+.RS 4
+Output sequences in input order (default is \-group)
+.RE
+.PP
+\fB\-group\fR
+.RS 4
+Group sequences by similarity (this is the default)
+.RE
+.PP
+\fB\-version\fR
+.RS 4
+Display version information and exit
+.RE
+.SH "SEE ALSO"
+.PP
+
+\fBclustalw\fR(1),
+\fBseaview\fR(1)\.
+.SH "AUTHORS"
+.PP
+\fBRobert Elgar\fR
+.sp -1n
+.IP "" 4
+Wrote Muscle\.
+.PP
+\fBSteffen Moeller\fR <\&moeller at debian\.org\&>
+.sp -1n
+.IP "" 4
+Wrote this manpage\.
+.PP
+\fBCharles Plessy\fR <\&charles\-debian\-nospam at plessy\.org\&>
+.sp -1n
+.IP "" 4
+Updated this manpage\.
+.SH "COPYRIGHT"
+Copyright \(co 2003, 2004 Steffen Moeller (manpage)
+.br
+Copyright \(co 2007 Charles Plessy (manpage)
+.br
+.PP
+Muscle is in the public domain, and therefore not subjected to copyright\.
+.PP
+This manual page was written by Steffen Moeller moeller at debian\.org for the
+Debian(TM)
+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\.
+.sp
Copied: trunk/packages/muscle/trunk/debian/muscle.1.xml (from rev 824, trunk/packages/muscle/trunk/debian/manpage.xml)
===================================================================
--- trunk/packages/muscle/trunk/debian/muscle.1.xml (rev 0)
+++ trunk/packages/muscle/trunk/debian/muscle.1.xml 2007-11-18 10:37:03 UTC (rev 832)
@@ -0,0 +1,256 @@
+<?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" [
+
+<!--
+
+Process this file with an XSLT processor: `xsltproc \
+-''-nonet /usr/share/sgml/docbook/stylesheet/xsl/nwalsh/\
+manpages/docbook.xsl manpage.dbk'. A manual page
+<package>.<section> will be generated. You may view the
+manual page with: nroff -man <package>.<section> | less'. A
+typical entry in a Makefile or Makefile.am is:
+
+DB2MAN=/usr/share/sgml/docbook/stylesheet/xsl/nwalsh/\
+manpages/docbook.xsl
+XP=xsltproc -''-nonet
+
+manpage.1: manpage.dbk
+ $(XP) $(DB2MAN) $<
+
+The xsltproc binary is found in the xsltproc package. The
+XSL files are in docbook-xsl. Please remember that if you
+create the nroff version in one of the debian/rules file
+targets (such as build), you will need to include xsltproc
+and docbook-xsl in your Build-Depends control field.
+
+-->
+
+ <!ENTITY dhfirstname "Steffen">
+ <!ENTITY dhsurname "Moeller">
+ <!ENTITY dhsection "<manvolnum>1</manvolnum>">
+ <!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>
+ <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>
+ <year>2004</year>
+ <holder>&dhusername; (manpage)</holder>
+ </copyright>
+ <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 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>
+
+ <para>This manual page documents briefly the
+ <command>&dhpackage;</command> command.
+ </para>
+
+ <para><command>&dhpackage;</command> aligns protein sequences and is considered superior and faster than clustalw.</para>
+ </refsect1>
+
+ <refsect1>
+ <title>OPTIONS</title>
+ <variablelist>
+ <varlistentry>
+ <term><option>-in <replaceable>input file</replaceable></option>
+ </term>
+ <listitem>
+ <para>Path to FASTA formatted input file
+ </para>
+ </listitem>
+ </varlistentry>
+ <varlistentry>
+ <term><option>-out <replaceable>output file</replaceable></option>
+ </term>
+ <listitem>
+ <para>Path to output file, FASTA formatted by default.
+ </para>
+ </listitem>
+ </varlistentry>
+ <varlistentry>
+ <term><option>-maxiters <replaceable>n</replaceable></option>
+ </term>
+ <listitem>
+ <para>Maximum number of iterations (integer, default 16)
+ </para>
+ </listitem>
+ </varlistentry>
+ <varlistentry>
+ <term><option>-maxhours <replaceable>n</replaceable></option>
+ </term>
+ <listitem>
+ <para>Maximum time to iterate in hours (default no limit)
+ </para>
+ </listitem>
+ </varlistentry>
+
+ <varlistentry>
+ <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 HTML format (default FASTA)</para>
+ </listitem>
+ </varlistentry>
+ <varlistentry>
+ <term><option>-msf</option>
+ </term>
+ <listitem>
+ <para>Write output in MSF format (default FASTA)</para>
+ </listitem>
+ </varlistentry>
+
+ <varlistentry>
+ <term><option>-clw</option>
+ </term>
+ <listitem>
+ <para>Write output in CLUSTALW format (default FASTA)</para>
+ </listitem>
+ </varlistentry>
+ <varlistentry>
+ <term><option>-clwstrict</option>
+ </term>
+ <listitem>
+ <para>As -clw, with 'CLUSTAL W (1.81)' header</para>
+ </listitem>
+ </varlistentry>
+
+ <varlistentry>
+ <term><option>-log[a] <replaceable>logfile</replaceable></option>
+ </term>
+ <listitem>
+ <para>Log to file (append if -loga, overwrite if -log)</para>
+ </listitem>
+ </varlistentry>
+ <varlistentry>
+ <term><option>-quiet</option>
+ </term>
+ <listitem>
+ <para>Do not write progress messages to stderr</para>
+ </listitem>
+ </varlistentry>
+ <varlistentry>
+ <term><option>-stable</option>
+ </term>
+ <listitem>
+ <para>Output sequences in input order (default is -group)</para>
+ </listitem>
+ </varlistentry>
+ <varlistentry>
+ <term><option>-group</option>
+ </term>
+ <listitem>
+ <para>Group sequences by similarity (this is the default)</para>
+ </listitem>
+ </varlistentry>
+ <varlistentry>
+ <term><option>-version</option>
+ </term>
+ <listitem>
+ <para>Display version information and exit</para>
+ </listitem>
+ </varlistentry>
+ </variablelist>
+ </refsect1>
+ <refsect1>
+ <title>SEE ALSO</title>
+ <para>
+ <citerefentry>
+ <refentrytitle>clustalw</refentrytitle>
+ <manvolnum>1</manvolnum>
+ </citerefentry>,
+
+ <citerefentry>
+ <refentrytitle>seaview</refentrytitle>
+ <manvolnum>1</manvolnum>
+ </citerefentry>.
+ </para>
+ </refsect1>
+</refentry>
Modified: trunk/packages/muscle/trunk/debian/rules
===================================================================
--- trunk/packages/muscle/trunk/debian/rules 2007-11-18 10:23:35 UTC (rev 831)
+++ trunk/packages/muscle/trunk/debian/rules 2007-11-18 10:37:03 UTC (rev 832)
@@ -6,9 +6,6 @@
# Uncomment this to turn on verbose mode.
#export DH_VERBOSE=1
-
-
-
CFLAGS = -Wall -g
ifneq (,$(findstring noopt,$(DEB_BUILD_OPTIONS)))
@@ -21,35 +18,32 @@
CFLAGS += -Winline
CFLAGS += -DNDEBUG=1
+DB2MAN=/usr/share/sgml/docbook/stylesheet/xsl/nwalsh/manpages/docbook.xsl
+XP=xsltproc -''-nonet -o debian/
+muscle.1: debian/muscle.1.xml
+ $(XP) $<
+
configure: configure-stamp
configure-stamp:
dh_testdir
- # Add here commands to configure the package.
+ touch $@
- touch configure-stamp
-
-
build: build-stamp
-
build-stamp: configure-stamp
dh_testdir
- # Add here commands to compile the package.
$(MAKE) CFLAGS="$(CFLAGS)"
- #/usr/bin/docbook-to-man debian/muscle.sgml > muscle.1
- xsltproc --nonet debian/manpage.xml
- touch build-stamp
+ touch $@
clean:
dh_testdir
dh_testroot
rm -f build-stamp configure-stamp
- # Add here commands to clean up after the build process.
[ ! -f Makefile ] || $(MAKE) clean
- dh_clean muscle.1
+ dh_clean
install: build
dh_testdir
@@ -57,7 +51,6 @@
dh_clean -k
dh_installdirs -a
- # Add here commands to install the package into debian/muscle.
$(MAKE) install DESTDIR=$(CURDIR)/debian/muscle
install-indep:
@@ -68,13 +61,12 @@
$(MAKE) install-doc DESTDIR=$(CURDIR)/debian/muscle-doc
-# Build architecture-independent files here.
binary-indep: install-indep
dh_testdir -i
dh_testroot -i
dh_installchangelogs -i
dh_installdocs -i
- dh_installman -i
+ dh_installman -i debian/muscle.1
dh_link -i
dh_strip -i
dh_compress -i
@@ -85,14 +77,13 @@
dh_md5sums -i
dh_builddeb -i
-# Build architecture-dependent files here.
binary-arch: build install
dh_testdir -a
dh_testroot -a
dh_installchangelogs -a
dh_installdocs -a
dh_installexamples -a
- dh_installman -a
+ dh_installman -a debian/muscle.1
dh_link -a
dh_strip -a
dh_compress -a
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