[med-svn] r307 - trunk/packages/mafft/trunk/debian
charles-guest at alioth.debian.org
charles-guest at alioth.debian.org
Sat Jun 9 14:28:06 UTC 2007
Author: charles-guest
Date: 2007-06-09 14:28:06 +0000 (Sat, 09 Jun 2007)
New Revision: 307
Added:
trunk/packages/mafft/trunk/debian/mafft.1.xml
Modified:
trunk/packages/mafft/trunk/debian/changelog
trunk/packages/mafft/trunk/debian/control
trunk/packages/mafft/trunk/debian/rules
Log:
New upstream release, manpage, changing recommends into suggests.
Modified: trunk/packages/mafft/trunk/debian/changelog
===================================================================
--- trunk/packages/mafft/trunk/debian/changelog 2007-06-04 13:27:59 UTC (rev 306)
+++ trunk/packages/mafft/trunk/debian/changelog 2007-06-09 14:28:06 UTC (rev 307)
@@ -1,6 +1,6 @@
-mafft (6.238-1) unstable; urgency=low
+mafft (6.240-1) unstable; urgency=low
* Initial release (Closes: #409640)
- -- Charles Plessy <charles-debian-nospam at plessy.org> Thu, 22 Mar 2007 23:11:56 +0900
+ -- Charles Plessy <charles-debian-nospam at plessy.org> Sat, 9 Jun 2007 12:06:43 +0900
Modified: trunk/packages/mafft/trunk/debian/control
===================================================================
--- trunk/packages/mafft/trunk/debian/control 2007-06-04 13:27:59 UTC (rev 306)
+++ trunk/packages/mafft/trunk/debian/control 2007-06-09 14:28:06 UTC (rev 307)
@@ -11,7 +11,7 @@
Package: mafft
Architecture: any
Depends: ${shlibs:Depends}, ${misc:Depends}
-Recommends: ruby
+Suggests: ruby, lynx
Description: Multiple alignment program for amino acid or nucleotide sequences
MAFFT is a multiple sequence alignment program, which offers three
accuracy-oriented methods:
Added: trunk/packages/mafft/trunk/debian/mafft.1.xml
===================================================================
--- trunk/packages/mafft/trunk/debian/mafft.1.xml (rev 0)
+++ trunk/packages/mafft/trunk/debian/mafft.1.xml 2007-06-09 14:28:06 UTC (rev 307)
@@ -0,0 +1,711 @@
+<?xml version='1.0' encoding='ISO-8859-1'?>
+<?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" [
+
+<!-- This manpage is based in the expample from the docbook-xsl
+ package version 1.72.0.dfsg.1-1 from Debian.-->
+
+ <!ENTITY dhfirstname "Charles">
+ <!ENTITY dhsurname "Plessy">
+ <!ENTITY dhemail "charles-debian-nospam at plessy.org">
+ <!ENTITY dhusername "&dhfirstname; &dhsurname;">
+ <!ENTITY dhrelease "6.240">
+ <!ENTITY dhdate "2007-06-09">
+ <!ENTITY dhtitle "Mafft Manual">
+ <!ENTITY dhucpackage "MAFFT">
+ <!ENTITY dhpackage "mafft">
+ <!ENTITY dhproduct "&dhpackage;">
+ <!ENTITY dhsection "1">
+]>
+
+<refentry>
+ <refentryinfo>
+ <title>&dhtitle;</title>
+ <productname>&dhpackage;</productname>
+ <releaseinfo role="version">&dhrelease;</releaseinfo>
+ <date>&dhdate;</date>
+ <authorgroup>
+ <author>
+ <firstname>Kazutaka</firstname>
+ <surname>Katoh</surname>
+ <contrib>Wrote Mafft.</contrib>
+ <address>
+ <email>katoh_at_bioreg.kyushu-u.ac.jp.</email>
+ </address>
+ </author>
+ <author>
+ <firstname>&dhfirstname;</firstname>
+ <surname>&dhsurname;</surname>
+ <contrib>Wrote this manpage in DocBook XML for the Debian distribution, using Mafft's homepage as a template.</contrib>
+ <address>
+ <email>&dhemail;</email>
+ </address>
+ </author>
+ </authorgroup>
+ <copyright>
+ <year>2002</year>
+ <year>2003</year>
+ <year>2004</year>
+ <year>2005</year>
+ <year>2006</year>
+ <year>2007</year>
+ <holder>Kazutaka Katoh</holder>
+ </copyright>
+ <copyright>
+ <year>2007</year>
+ <holder>&dhusername;</holder>
+ </copyright>
+ <legalnotice>
+ <para>Mafft and its manpage are offered under the following conditions:</para>
+ <para>Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met:</para>
+ <orderedlist>
+ <listitem>
+ <para>Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer.</para>
+ </listitem>
+ <listitem>
+ <para>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.</para>
+ </listitem>
+ <listitem>
+ <para>The name of the author may not be used to endorse or promote products derived from this software without specific prior written permission.</para>
+ </listitem>
+ </orderedlist>
+ <para>THIS SOFTWARE IS PROVIDED BY THE AUTHOR "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 AUTHOR 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.</para>
+ </legalnotice>
+ </refentryinfo>
+
+ <refmeta>
+ <refentrytitle>&dhucpackage;</refentrytitle>
+ <manvolnum>&dhsection;</manvolnum>
+ </refmeta>
+
+ <refnamediv>
+ <refname>&dhpackage;</refname>
+ <refpurpose>Multiple alignment program for amino acid or nucleotide sequences</refpurpose>
+ </refnamediv>
+
+ <refsynopsisdiv>
+ <cmdsynopsis>
+ <command>&dhpackage;</command>
+ <arg choice="opt"><option>options</option></arg>
+ <arg choice="plain"><replaceable>input</replaceable></arg>
+ <arg choice="opt">> <replaceable>output</replaceable></arg>
+ </cmdsynopsis>
+
+ <cmdsynopsis>
+ <command>linsi</command>
+ <arg choice="plain"><replaceable>input</replaceable></arg>
+ <arg choice="opt">> <replaceable>output</replaceable></arg>
+ </cmdsynopsis>
+
+ <cmdsynopsis>
+ <command>ginsi</command>
+ <arg choice="plain"><replaceable>input</replaceable></arg>
+ <arg choice="opt">> <replaceable>output</replaceable></arg>
+ </cmdsynopsis>
+
+ <cmdsynopsis>
+ <command>einsi</command>
+ <arg choice="plain"><replaceable>input</replaceable></arg>
+ <arg choice="opt">> <replaceable>output</replaceable></arg>
+ </cmdsynopsis>
+
+ <cmdsynopsis>
+ <command>fftnsi</command>
+ <arg choice="plain"><replaceable>input</replaceable></arg>
+ <arg choice="opt">> <replaceable>output</replaceable></arg>
+ </cmdsynopsis>
+
+ <cmdsynopsis>
+ <command>fftns</command>
+ <arg choice="plain"><replaceable>input</replaceable></arg>
+ <arg choice="opt">> <replaceable>output</replaceable></arg>
+ </cmdsynopsis>
+
+ <cmdsynopsis>
+ <command>mafft-profile</command>
+ <arg choice="plain"><replaceable>group1</replaceable></arg>
+ <arg choice="plain"><replaceable>group2</replaceable></arg>
+ <arg choice="opt">> <replaceable>output</replaceable></arg>
+ </cmdsynopsis>
+ </refsynopsisdiv>
+
+ <refsect1 id="description">
+ <title>DESCRIPTION</title>
+
+ <para><command>&dhucpackage;</command> is a multiple sequence alignment program for unix-like operating systems. It offers a range of multiple alignment methods.</para>
+
+ <refsect2>
+ <title>Accuracy-oriented methods:</title>
+ <itemizedlist>
+ <listitem>
+ <para>L-INS-i (probably most accurate; recommended for <200 sequences; iterative refinement method incorporating local pairwise alignment information):</para>
+
+ <cmdsynopsis>
+ <command>&dhpackage;</command>
+ <arg choice="plain"><option>--localpair</option></arg>
+ <arg choice="plain">
+ <option>--maxiterate</option>
+ <replaceable>1000</replaceable>
+ </arg>
+ <arg choice="plain"><replaceable>input</replaceable></arg>
+ <arg choice="opt">> <replaceable>output</replaceable></arg>
+ </cmdsynopsis>
+
+ <cmdsynopsis>
+ <command>linsi</command>
+ <arg choice="plain"><replaceable>input</replaceable></arg>
+ <arg choice="opt">> <replaceable>output</replaceable></arg>
+ </cmdsynopsis>
+ </listitem>
+
+ <listitem>
+ <para>G-INS-i (suitable for sequences of similar lengths; recommended for <200 sequences; iterative refinement method incorporating global pairwise alignment information):</para>
+
+ <cmdsynopsis>
+ <command>&dhpackage;</command>
+ <arg choice="plain"><option>--globalpair</option></arg>
+ <arg choice="plain">
+ <option>--maxiterate</option>
+ <replaceable>1000</replaceable>
+ </arg>
+ <arg choice="plain"><replaceable>input</replaceable></arg>
+ <arg choice="opt">> <replaceable>output</replaceable></arg>
+ </cmdsynopsis>
+
+ <cmdsynopsis>
+ <command>ginsi</command>
+ <arg choice="plain"><replaceable>input</replaceable></arg>
+ <arg choice="opt">> <replaceable>output</replaceable></arg>
+ </cmdsynopsis>
+ </listitem>
+
+ <listitem>
+ <para>E-INS-i (suitable for sequences containing large unalignable regions; recommended for <200 sequences):</para>
+
+ <cmdsynopsis>
+ <command>&dhpackage;</command>
+ <arg choice="plain">
+ <option>--ep</option>
+ <replaceable>0</replaceable>
+ </arg>
+ <arg choice="plain"><option>--genafpair</option></arg>
+ <arg choice="plain">
+ <option>--maxiterate</option>
+ <replaceable>1000</replaceable>
+ </arg>
+ <arg choice="plain"><replaceable>input</replaceable></arg>
+ <arg choice="opt">> <replaceable>output</replaceable></arg>
+ </cmdsynopsis>
+
+ <cmdsynopsis>
+ <command>einsi</command>
+ <arg choice="plain"><replaceable>input</replaceable></arg>
+ <arg choice="opt">> <replaceable>output</replaceable></arg>
+ <sbr/>
+ </cmdsynopsis>
+
+ <para>For E-INS-i, the <option>--ep</option> <replaceable>0</replaceable> option is recommended to allow large gaps.</para>
+ </listitem>
+ </itemizedlist>
+ </refsect2>
+
+ <refsect2>
+ <title>Speed-oriented methods:</title>
+ <itemizedlist>
+ <listitem>
+ <para>FFT-NS-i (iterative refinement method; two cycles only):</para>
+ <cmdsynopsis>
+ <command>&dhpackage;</command>
+ <arg choice="plain">
+ <option>--retree</option>
+ <replaceable>2</replaceable>
+ </arg>
+ <arg choice="plain">
+ <option>--maxiterate</option>
+ <replaceable>2</replaceable>
+ </arg>
+ <arg choice="plain"><replaceable>input</replaceable></arg>
+ <arg choice="opt">> <replaceable>output</replaceable></arg>
+ </cmdsynopsis>
+
+ <cmdsynopsis>
+ <command>fftnsi</command>
+ <arg choice="plain"><replaceable>input</replaceable></arg>
+ <arg choice="opt">> <replaceable>output</replaceable></arg>
+ </cmdsynopsis>
+ </listitem>
+
+ <listitem>
+ <para>FFT-NS-i (iterative refinement method; max. 1000 iterations): </para>
+ <cmdsynopsis>
+ <command>&dhpackage;</command>
+ <arg choice="plain">
+ <option>--retree</option>
+ <replaceable>2</replaceable>
+ </arg>
+ <arg choice="plain">
+ <option>--maxiterate</option>
+ <replaceable>1000</replaceable>
+ </arg>
+ <arg choice="plain"><replaceable>input</replaceable></arg>
+ <arg choice="opt">> <replaceable>output</replaceable></arg>
+ </cmdsynopsis>
+ </listitem>
+
+ <listitem>
+ <para>FFT-NS-2 (fast; progressive method):</para>
+ <cmdsynopsis>
+ <command>&dhpackage;</command>
+ <arg choice="plain">
+ <option>--retree</option>
+ <replaceable>2</replaceable>
+ </arg>
+ <arg choice="plain">
+ <option>--maxiterate</option>
+ <replaceable>0</replaceable>
+ </arg>
+ <arg choice="plain"><replaceable>input</replaceable></arg>
+ <arg choice="opt">> <replaceable>output</replaceable></arg>
+ </cmdsynopsis>
+
+ <cmdsynopsis>
+ <command>fftns</command>
+ <arg choice="plain"><replaceable>input</replaceable></arg>
+ <arg choice="opt">> <replaceable>output</replaceable></arg>
+ </cmdsynopsis>
+ </listitem>
+
+ <listitem>
+ <para>FFT-NS-1 (very fast; recommended for >2000 sequences; progressive method with a rough guide tree):</para>
+
+ <cmdsynopsis>
+ <command>&dhpackage;</command>
+ <arg choice="plain">
+ <option>--retree</option>
+ <replaceable>1</replaceable>
+ </arg>
+ <arg choice="plain">
+ <option>--maxiterate</option>
+ <replaceable>0</replaceable>
+ </arg>
+ <arg choice="plain"><replaceable>input</replaceable></arg>
+ <arg choice="opt">> <replaceable>output</replaceable></arg>
+ </cmdsynopsis>
+ </listitem>
+
+ <listitem>
+ <para>NW-NS-PartTree-1 (recommended for ?50,000 sequences; progressive method with the PartTree algorithm):</para>
+
+ <cmdsynopsis>
+ <command>&dhpackage;</command>
+ <arg choice="plain">
+ <option>--retree</option>
+ <replaceable>1</replaceable>
+ </arg>
+ <arg choice="plain">
+ <option>--maxiterate</option>
+ <replaceable>0</replaceable>
+ </arg>
+ <arg choice="plain"><option>--parttree</option></arg>
+ <arg choice="plain"><replaceable>input</replaceable></arg>
+ <arg choice="opt">> <replaceable>output</replaceable></arg>
+ </cmdsynopsis>
+ </listitem>
+ </itemizedlist>
+ </refsect2>
+
+ <refsect2>
+ <title>Group-to-group alignments</title>
+
+ <cmdsynopsis>
+ <command>mafft-profile</command>
+ <arg choice="plain"><replaceable>group1</replaceable></arg>
+ <arg choice="plain"><replaceable>group2</replaceable></arg>
+ <arg choice="opt">> <replaceable>output</replaceable></arg>
+ </cmdsynopsis>
+
+ <para>or:</para>
+
+ <cmdsynopsis>
+ <command>&dhpackage;</command>
+ <arg choice="plain">
+ <option>--maxiterate</option>
+ <replaceable>1000</replaceable>
+ </arg>
+ <arg choice="plain">
+ <option>--seed</option>
+ <replaceable>group1</replaceable>
+ </arg>
+ <arg choice="plain">
+ <option>--seed</option>
+ <replaceable>group2</replaceable>
+ </arg>
+ <arg choice="plain">/dev/null</arg>
+ <arg choice="opt">> <replaceable>output</replaceable></arg>
+ </cmdsynopsis>
+ </refsect2>
+ </refsect1>
+
+ <refsect1 id="options">
+ <title>OPTIONS</title>
+ <variablelist>
+ <!-- Use the variablelist.term.separator and the
+ variablelist.term.break.after parameters to
+ control the term elements. -->
+ <varlistentry>
+ <term><option>--auto</option></term>
+ <listitem>
+ <para></para>
+ </listitem>
+ </varlistentry>
+
+ <varlistentry>
+ <term><option>--clustalout</option></term>
+ <listitem>
+ <para></para>
+ </listitem>
+ </varlistentry>
+
+ <varlistentry>
+ <term><option>--reorder</option></term>
+ <listitem>
+ <para></para>
+ </listitem>
+ </varlistentry>
+
+ <varlistentry>
+ <term><option>--inputorder</option></term>
+ <listitem>
+ <para></para>
+ </listitem>
+ </varlistentry>
+
+ <varlistentry>
+ <term><option>--algq</option></term>
+ <listitem>
+ <para></para>
+ </listitem>
+ </varlistentry>
+
+ <varlistentry>
+ <term><option>--groupsize</option></term>
+ <listitem>
+ <para></para>
+ </listitem>
+ </varlistentry>
+
+ <varlistentry>
+ <term><option>--partsize</option></term>
+ <listitem>
+ <para></para>
+ </listitem>
+ </varlistentry>
+
+ <varlistentry>
+ <term><option>--parttree</option></term>
+ <listitem>
+ <para></para>
+ </listitem>
+ </varlistentry>
+
+ <varlistentry>
+ <term><option>--dpparttree</option></term>
+ <listitem>
+ <para></para>
+ </listitem>
+ </varlistentry>
+
+ <varlistentry>
+ <term><option>--fastaparttree</option></term>
+ <listitem>
+ <para></para>
+ </listitem>
+ </varlistentry>
+
+ <varlistentry>
+ <term><option>--treeout</option></term>
+ <listitem>
+ <para></para>
+ </listitem>
+ </varlistentry>
+
+ <varlistentry>
+ <term><option>--fastswpair</option></term>
+ <listitem>
+ <para></para>
+ </listitem>
+ </varlistentry>
+
+ <varlistentry>
+ <term><option>--fastapair</option></term>
+ <listitem>
+ <para></para>
+ </listitem>
+ </varlistentry>
+
+ <varlistentry>
+ <term><option>--noscore</option></term>
+ <listitem>
+ <para></para>
+ </listitem>
+ </varlistentry>
+
+ <varlistentry>
+ <term><option>--6merpair</option></term>
+ <listitem>
+ <para></para>
+ </listitem>
+ </varlistentry>
+
+ <varlistentry>
+ <term><option>--blastpair</option></term>
+ <listitem>
+ <para></para>
+ </listitem>
+ </varlistentry>
+
+ <varlistentry>
+ <term><option>--globalpair</option></term>
+ <listitem>
+ <para></para>
+ </listitem>
+ </varlistentry>
+
+ <varlistentry>
+ <term><option>--localpair</option></term>
+ <listitem>
+ <para></para>
+ </listitem>
+ </varlistentry>
+
+ <varlistentry>
+ <term><option>--genafpair</option></term>
+ <listitem>
+ <para></para>
+ </listitem>
+ </varlistentry>
+
+ <varlistentry>
+ <term><option>--memsave</option></term>
+ <listitem>
+ <para></para>
+ </listitem>
+ </varlistentry>
+
+ <varlistentry>
+ <term><option>--nuc</option></term>
+ <listitem>
+ <para></para>
+ </listitem>
+ </varlistentry>
+
+ <varlistentry>
+ <term><option>--amino</option></term>
+ <listitem>
+ <para></para>
+ </listitem>
+ </varlistentry>
+
+ <varlistentry>
+ <term><option>--fft</option></term>
+ <listitem>
+ <para></para>
+ </listitem>
+ </varlistentry>
+
+ <varlistentry>
+ <term><option>--nofft</option></term>
+ <listitem>
+ <para></para>
+ </listitem>
+ </varlistentry>
+
+ <varlistentry>
+ <term><option>--quiet</option></term>
+ <listitem>
+ <para></para>
+ </listitem>
+ </varlistentry>
+
+ <varlistentry>
+ <term><option>--coreext</option></term>
+ <listitem>
+ <para></para>
+ </listitem>
+ </varlistentry>
+
+ <varlistentry>
+ <term><option>--core</option></term>
+ <listitem>
+ <para></para>
+ </listitem>
+ </varlistentry>
+
+ <varlistentry>
+ <term><option>--maxiterate</option></term>
+ <listitem>
+ <para></para>
+ </listitem>
+ </varlistentry>
+
+ <varlistentry>
+ <term><option>--retree</option></term>
+ <listitem>
+ <para></para>
+ </listitem>
+ </varlistentry>
+
+ <varlistentry>
+ <term><option>--aamatrix</option></term>
+ <listitem>
+ <para></para>
+ </listitem>
+ </varlistentry>
+
+ <varlistentry>
+ <term><option>--fmodel</option></term>
+ <listitem>
+ <para></para>
+ </listitem>
+ </varlistentry>
+
+ <varlistentry>
+ <term><option>--jtt</option></term>
+ <listitem>
+ <para></para>
+ </listitem>
+ </varlistentry>
+
+ <varlistentry>
+ <term><option>--tm</option></term>
+ <listitem>
+ <para></para>
+ </listitem>
+ </varlistentry>
+
+ <varlistentry>
+ <term><option>--bl</option></term>
+ <listitem>
+ <para></para>
+ </listitem>
+ </varlistentry>
+
+ <varlistentry>
+ <term><option>--weighti</option></term>
+ <listitem>
+ <para></para>
+ </listitem>
+ </varlistentry>
+
+ <varlistentry>
+ <term><option>--op</option></term>
+ <listitem>
+ <para></para>
+ </listitem>
+ </varlistentry>
+
+ <varlistentry>
+ <term><option>--ep</option></term>
+ <listitem>
+ <para></para>
+ </listitem>
+ </varlistentry>
+
+ <varlistentry>
+ <term><option>--lop</option></term>
+ <listitem>
+ <para></para>
+ </listitem>
+ </varlistentry>
+
+ <varlistentry>
+ <term><option>--LOP</option></term>
+ <listitem>
+ <para></para>
+ </listitem>
+ </varlistentry>
+
+ <varlistentry>
+ <term><option>--lep</option></term>
+ <listitem>
+ <para></para>
+ </listitem>
+ </varlistentry>
+
+ <varlistentry>
+ <term><option>--lexp</option></term>
+ <listitem>
+ <para></para>
+ </listitem>
+ </varlistentry>
+
+ <varlistentry>
+ <term><option>--LEXP</option></term>
+ <listitem>
+ <para></para>
+ </listitem>
+ </varlistentry>
+
+ <varlistentry>
+ <term><option>--corethr</option></term>
+ <listitem>
+ <para></para>
+ </listitem>
+ </varlistentry>
+
+ <varlistentry>
+ <term><option>--corewin</option></term>
+ <listitem>
+ <para></para>
+ </listitem>
+ </varlistentry>
+
+ <varlistentry>
+ <term><option>--seed</option></term>
+ <listitem>
+ <para></para>
+ </listitem>
+ </varlistentry>
+ </variablelist>
+ </refsect1>
+
+ <refsect1 id="files">
+ <title>FILES</title>
+ <variablelist>
+ <varlistentry>
+ <term><filename>/etc/foo.conf</filename></term>
+ <listitem>
+ <para>The system-wide configuration file. See <citerefentry><refentrytitle>foo.conf</refentrytitle><manvolnum>5</manvolnum></citerefentry> for further details.</para>
+ </listitem>
+ </varlistentry>
+ <varlistentry>
+ <term><filename>${HOME}/.foo.conf</filename></term>
+ <listitem>
+ <para>The per-user configuration file. See <citerefentry><refentrytitle>foo.conf</refentrytitle><manvolnum>5</manvolnum></citerefentry> for further details.</para>
+ </listitem>
+ </varlistentry>
+ </variablelist>
+ </refsect1>
+
+ <refsect1 id="see_also">
+ <title>SEE ALSO</title>
+ <!-- In alpabetical order. -->
+ <para><citerefentry>
+ <refentrytitle>bar</refentrytitle>
+ <manvolnum>1</manvolnum>
+ </citerefentry>, <citerefentry>
+ <refentrytitle>foo</refentrytitle>
+ <manvolnum>1</manvolnum>
+ </citerefentry>, <citerefentry>
+ <refentrytitle>foo.conf</refentrytitle>
+ <manvolnum>5</manvolnum>
+ </citerefentry>, <citerefentry>
+ <refentrytitle>xyzzy</refentrytitle>
+ <manvolnum>1</manvolnum>
+ </citerefentry></para>
+ <para>The programs are documented fully by <citetitle>The Rise and Fall of a Fooish Bar</citetitle> available via the <application>Info</application> system.</para>
+ </refsect1>
+</refentry>
+
Modified: trunk/packages/mafft/trunk/debian/rules
===================================================================
--- trunk/packages/mafft/trunk/debian/rules 2007-06-04 13:27:59 UTC (rev 306)
+++ trunk/packages/mafft/trunk/debian/rules 2007-06-09 14:28:06 UTC (rev 307)
@@ -20,16 +20,18 @@
CFLAGS += -O2
endif
-manpages: debian/mafft.1.xml
+mafft.1: debian/mafft.1.xml
$(XP) $<
-build: manpages
+build-stamp: build
+build: mafft.1
dh_testdir
$(MAKE) -C src PREFIX=/usr/lib/mafft
+ touch build-stamp
MAFFT = MAFFT_BINARIES=$(CURDIR)/binaries scripts/mafft
-test: build
+test: build-stamp
-$(MAFFT) test/sample | diff test/sample.fftns2 -
-$(MAFFT) --maxiterate 100 test/sample | diff test/sample.fftnsi -
-$(MAFFT) --globalpair test/sample | diff test/sample.gins1 -
@@ -41,9 +43,9 @@
dh_testdir
dh_testroot
-$(MAKE) -C src clean
- dh_clean mafft.1
+ dh_clean mafft.1 build-stamp
-install: build test
+install: build-stamp test
dh_testdir
dh_testroot
dh_clean -k
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