[med-svn] r308 - trunk/packages/mafft/trunk/debian
charles-guest at alioth.debian.org
charles-guest at alioth.debian.org
Sun Jun 10 02:48:57 UTC 2007
Author: charles-guest
Date: 2007-06-10 02:48:57 +0000 (Sun, 10 Jun 2007)
New Revision: 308
Added:
trunk/packages/mafft/trunk/debian/links
trunk/packages/mafft/trunk/debian/mafft-homologs.1.xml
Modified:
trunk/packages/mafft/trunk/debian/control
trunk/packages/mafft/trunk/debian/mafft.1.xml
trunk/packages/mafft/trunk/debian/rules
Log:
One more manpage, fixing lintian errors, adding a suggested package.
Modified: trunk/packages/mafft/trunk/debian/control
===================================================================
--- trunk/packages/mafft/trunk/debian/control 2007-06-09 14:28:06 UTC (rev 307)
+++ trunk/packages/mafft/trunk/debian/control 2007-06-10 02:48:57 UTC (rev 308)
@@ -11,7 +11,7 @@
Package: mafft
Architecture: any
Depends: ${shlibs:Depends}, ${misc:Depends}
-Suggests: ruby, lynx
+Suggests: ruby, lynx, blast2
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/links
===================================================================
--- trunk/packages/mafft/trunk/debian/links (rev 0)
+++ trunk/packages/mafft/trunk/debian/links 2007-06-10 02:48:57 UTC (rev 308)
@@ -0,0 +1,14 @@
+usr/share/man/man1/mafft.1 /usr/share/man/man1/mafft-linsi.1
+usr/share/man/man1/mafft.1 usr/share/man/man1/mafft-ginsi.1
+usr/share/man/man1/mafft.1 usr/share/man/man1/mafft-einsi.1
+usr/share/man/man1/mafft.1 usr/share/man/man1/mafft-fftnsi.1
+usr/share/man/man1/mafft.1 usr/share/man/man1/mafft-fftns.1
+
+usr/share/man/man1/mafft.1 usr/share/man/man1/linsi.1
+usr/share/man/man1/mafft.1 usr/share/man/man1/ginsi.1
+usr/share/man/man1/mafft.1 usr/share/man/man1/einsi.1
+usr/share/man/man1/mafft.1 usr/share/man/man1/fftnsi.1
+usr/share/man/man1/mafft.1 usr/share/man/man1/fftns.1
+
+usr/share/man/man1/mafft.1 usr/share/man/man1/mafft-profile.1
+
Added: trunk/packages/mafft/trunk/debian/mafft-homologs.1.xml
===================================================================
--- trunk/packages/mafft/trunk/debian/mafft-homologs.1.xml (rev 0)
+++ trunk/packages/mafft/trunk/debian/mafft-homologs.1.xml 2007-06-10 02:48:57 UTC (rev 308)
@@ -0,0 +1,194 @@
+<?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" [
+
+<!-- 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 "2.1">
+ <!ENTITY dhdate "2007-06-09">
+ <!ENTITY dhtitle "Mafft Manual">
+ <!ENTITY dhucpackage "MAFFT-HOMOLOGS">
+ <!ENTITY dhpackage "mafft-homologs">
+ <!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 (mafft)</holder>
+ </copyright>
+ <copyright>
+ <year>2007</year>
+ <holder>&dhusername; (this manpage)</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>aligns sequences together with homologues automatically collected from SwissProt via NCBI BLAST</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>
+ </refsynopsisdiv>
+
+ <refsect1 id="description">
+ <title>DESCRIPTION</title>
+ <para>The accuracy of an alignment of a few distantly related sequences is considerably improved when being aligned together with their close homologs. The reason for the improvement is probably the same as that for PSI-BLAST. That is, the positions of highly conserved residues, those with many gaps and other additional information is brought by close homologs. According to Katoh et al. (2005), the improvement by adding close homologs is 10% or so, which is comparable to the improvement by incorporating structural information of a pair of sequences. Mafft-homologs in a mafft server works like this:</para>
+ <orderedlist>
+ <listitem>
+ <para>Collect a number (50 by default) of close homologs (E=1e-10 by default) of the input sequences.</para>
+ </listitem>
+
+ <listitem>
+ <para>Align the input sequences and homologs all together using the L-INS-i strategy.</para>
+ </listitem>
+
+ <listitem>
+ <para>Remove the homologs.</para>
+ </listitem>
+ </orderedlist>
+ </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>-a</option>
+ <varname><replaceable>n</replaceable></varname>
+ </term>
+ <listitem>
+ <para>The number of collected sequences (default: 50).</para>
+ </listitem>
+ </varlistentry>
+
+ <varlistentry>
+ <term>
+ <option>-e</option>
+ <varname><replaceable>n</replaceable></varname>
+ </term>
+ <listitem>
+ <para>Threshold value (default: 1e-10).</para>
+ </listitem>
+ </varlistentry>
+
+ <varlistentry>
+ <term>
+ <option>-o</option>
+ <varname><replaceable>xxx</replaceable></varname>
+ </term>
+ <listitem>
+ <para>options for mafft (default: " --op 1.53 --ep 0.123 --maxiterate 1000").</para>
+ </listitem>
+ </varlistentry>
+
+ <varlistentry>
+ <term><option>-l</option></term>
+ <listitem>
+ <para>Locally carries out blast searches instead of NCBI blast (requires locally installed blast and a database).</para>
+ </listitem>
+ </varlistentry>
+
+ <varlistentry>
+ <term><option>-f</option></term>
+ <listitem>
+ <para>Outputs collected homologues also (default: off).</para>
+ </listitem>
+ </varlistentry>
+
+ <varlistentry>
+ <term><option>-w</option></term>
+ <listitem>
+ <para>entire sequences are subjected to BLAST search (default: well-aligned region only)</para>
+ </listitem>
+ </varlistentry>
+ </variablelist>
+ </refsect1>
+
+ <refsect1 id="files">
+ <title>REQUIREMENTS</title>
+ <para>Mafft-homologs requires a version of mafft higher than 5.58.</para>
+ </refsect1>
+
+ <refsect1 id="references">
+ <title>REFERENCES</title>
+ <para>Katoh, Kuma, Toh and Miyata (Nucleic Acids Res. 33:511-518, 2005) MAFFT version 5: improvement in accuracy of multiple sequence alignment.</para>
+ </refsect1>
+
+ <refsect1 id="see_also">
+ <title>SEE ALSO</title>
+ <!-- In alpabetical order. -->
+ <para>
+ <citerefentry>
+ <refentrytitle>mafft</refentrytitle>
+ <manvolnum>1</manvolnum>
+ </citerefentry>
+ </para>
+ </refsect1>
+</refentry>
Modified: trunk/packages/mafft/trunk/debian/mafft.1.xml
===================================================================
--- trunk/packages/mafft/trunk/debian/mafft.1.xml 2007-06-09 14:28:06 UTC (rev 307)
+++ trunk/packages/mafft/trunk/debian/mafft.1.xml 2007-06-10 02:48:57 UTC (rev 308)
@@ -1,4 +1,4 @@
-<?xml version='1.0' encoding='ISO-8859-1'?>
+<?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"
@@ -51,11 +51,11 @@
<year>2005</year>
<year>2006</year>
<year>2007</year>
- <holder>Kazutaka Katoh</holder>
+ <holder>Kazutaka Katoh (mafft)</holder>
</copyright>
<copyright>
<year>2007</year>
- <holder>&dhusername;</holder>
+ <holder>&dhusername; (this manpage)</holder>
</copyright>
<legalnotice>
<para>Mafft and its manpage are offered under the following conditions:</para>
@@ -673,39 +673,70 @@
<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>
+ <para>Mafft stores the input sequences and other files in a temporary directory, which by default is located in <filename class="directory">/tmp</filename>.</para>
</refsect1>
+ <refsect1 id="environment">
+ <title>ENVIONMENT</title>
+ <variablelist>
+ <varlistentry>
+ <term><envar>MAFFT_BINARIES</envar></term>
+ <listitem>
+ <para>Indicates the location of the binary files used by mafft. By default, they are searched in <filename class="directory">/usr/local/lib/mafft</filename>, but on Debian systems, they are searched in <filename class="directory">/usr/lib/mafft</filename>.</para>
+ </listitem>
+ </varlistentry>
+
+ <varlistentry>
+ <term><envar>FASTA_4_MAFFT</envar></term>
+ <listitem>
+ <para>This variable can be set to indicate to mafft the location to the fasta34 program if it is not in the PATH.</para>
+ </listitem>
+ </varlistentry>
+ </variablelist>
+ </refsect1>
+
<refsect1 id="see_also">
<title>SEE ALSO</title>
<!-- In alpabetical order. -->
- <para><citerefentry>
- <refentrytitle>bar</refentrytitle>
+ <para>
+ <citerefentry>
+ <refentrytitle>mafft-homologs</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>
+ </citerefentry>
+ </para>
</refsect1>
+
+ <refsect1 id="references">
+ <title>REFERENCES</title>
+ <refsect2>
+ <title>In English</title>
+ <itemizedlist>
+ <listitem>
+ <para>Katoh and Toh (Bioinformatics 23:372-374, 2007) PartTree: an algorithm to build an approximate tree from a large number of unaligned sequences (describes the PartTree algorithm).</para>
+ </listitem>
+
+ <listitem>
+ <para>Katoh, Kuma, Toh and Miyata (Nucleic Acids Res. 33:511-518, 2005) MAFFT version 5: improvement in accuracy of multiple sequence alignment (describes [ancestral versions of] the G-INS-i, L-INS-i and E-INS-i strategies)</para>
+ </listitem>
+
+ <listitem>
+ <para>Katoh, Misawa, Kuma and Miyata (Nucleic Acids Res. 30:3059-3066, 2002) MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform (describes the FFT-NS-1, FFT-NS-2 and FFT-NS-i strategies)</para>
+ </listitem>
+ </itemizedlist>
+ </refsect2>
+
+ <refsect2>
+ <title>In Japanese</title>
+ <itemizedlist>
+ <listitem>
+ <para>Katoh and Misawa (???? 46:312-317, 2006) Multiple Sequence Alignments: the Next Generation</para>
+ </listitem>
+
+ <listitem>
+ <para>Katoh and Kuma (????? 44:102-108, 2006) Jissen-teki Multiple Alignment</para>
+ </listitem>
+ </itemizedlist>
+ </refsect2>
+ </refsect1>
</refentry>
Modified: trunk/packages/mafft/trunk/debian/rules
===================================================================
--- trunk/packages/mafft/trunk/debian/rules 2007-06-09 14:28:06 UTC (rev 307)
+++ trunk/packages/mafft/trunk/debian/rules 2007-06-10 02:48:57 UTC (rev 308)
@@ -23,8 +23,11 @@
mafft.1: debian/mafft.1.xml
$(XP) $<
+mafft-homologs.1: debian/mafft-homologs.1.xml
+ $(XP) $<
+
build-stamp: build
-build: mafft.1
+build: mafft.1 mafft-homologs.1
dh_testdir
$(MAKE) -C src PREFIX=/usr/lib/mafft
touch build-stamp
@@ -43,7 +46,7 @@
dh_testdir
dh_testroot
-$(MAKE) -C src clean
- dh_clean mafft.1 build-stamp
+ dh_clean mafft.1 mafft-homologs.1 build-stamp
install: build-stamp test
dh_testdir
@@ -51,6 +54,7 @@
dh_clean -k
dh_installdirs
$(MAKE) -C src PREFIX=$(CURDIR)/debian/mafft/usr/lib/mafft install
+ mv debian/mafft/usr/bin/mafft-homologs.rb debian/mafft/usr/bin/mafft-homologs
binary-indep: build install
@@ -60,7 +64,7 @@
dh_installchangelogs
dh_installdocs
dh_install test usr/share/doc/mafft/
- dh_installman mafft.1
+ dh_installman mafft.1 mafft-homologs.1
dh_link
dh_strip
dh_compress
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