[med-svn] r214 - trunk/packages/kalign/trunk/debian
Charles Plessy
charles-guest at alioth.debian.org
Mon Feb 19 13:48:34 CET 2007
Author: charles-guest
Date: 2007-02-19 13:48:33 +0100 (Mon, 19 Feb 2007)
New Revision: 214
Removed:
trunk/packages/kalign/trunk/debian/dirs
trunk/packages/kalign/trunk/debian/docs
trunk/packages/kalign/trunk/debian/manpages
Modified:
trunk/packages/kalign/trunk/debian/copyright
trunk/packages/kalign/trunk/debian/kalign.1.xml
trunk/packages/kalign/trunk/debian/rules
trunk/packages/kalign/trunk/debian/watch
Log:
Updating manpages and authors email, tidying building.
Modified: trunk/packages/kalign/trunk/debian/copyright
===================================================================
--- trunk/packages/kalign/trunk/debian/copyright 2007-02-17 09:25:42 UTC (rev 213)
+++ trunk/packages/kalign/trunk/debian/copyright 2007-02-19 12:48:33 UTC (rev 214)
@@ -1,4 +1,4 @@
-Copyright (C) 2006 Timo Lassmann <timolassmann at gmail.com>
+Copyright (C) 2004, 2005, 2006 Timo Lassmann <timolassmann at gmail.com>
License:
Deleted: trunk/packages/kalign/trunk/debian/dirs
===================================================================
--- trunk/packages/kalign/trunk/debian/dirs 2007-02-17 09:25:42 UTC (rev 213)
+++ trunk/packages/kalign/trunk/debian/dirs 2007-02-19 12:48:33 UTC (rev 214)
@@ -1 +0,0 @@
-/usr/bin
Deleted: trunk/packages/kalign/trunk/debian/docs
===================================================================
--- trunk/packages/kalign/trunk/debian/docs 2007-02-17 09:25:42 UTC (rev 213)
+++ trunk/packages/kalign/trunk/debian/docs 2007-02-19 12:48:33 UTC (rev 214)
@@ -1 +0,0 @@
-README
Modified: trunk/packages/kalign/trunk/debian/kalign.1.xml
===================================================================
--- trunk/packages/kalign/trunk/debian/kalign.1.xml 2007-02-17 09:25:42 UTC (rev 213)
+++ trunk/packages/kalign/trunk/debian/kalign.1.xml 2007-02-19 12:48:33 UTC (rev 214)
@@ -1,16 +1,16 @@
<?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>avril 29, 2006</date>">
+ <!ENTITY dhdate "February 17, 2007">
<!ENTITY dhsection "<manvolnum>1</manvolnum>">
<!ENTITY dhemail "<email>charles-debian-nospam at plessy.org</email>">
<!ENTITY dhusername "Charles Plessy">
<!ENTITY dhucpackage "<refentrytitle>KALIGN</refentrytitle>">
<!ENTITY dhpackage "kalign">
+ <!ENTITY dhrelease "2.03">
+ <!ENTITY dhtitle "Kalign User Manual">
<!ENTITY debian "<productname>Debian</productname>">
<!ENTITY gnu "<acronym>GNU</acronym>">
<!ENTITY gpl "&gnu; <acronym>GPL</acronym>">
@@ -20,6 +20,10 @@
<refentry>
<refentryinfo>
+ <title>&dhtitle;</title>
+ <productname>&dhpackage;</productname>
+ <releaseinfo role="version">&dhrelease;</releaseinfo>
+ <date>&dhdate;</date>
<address>
&dhemail;
</address>
@@ -31,7 +35,6 @@
<year>2006</year>
<holder>&dhusername;</holder>
</copyright>
- &dhdate;
</refentryinfo>
<refmeta>
&dhucpackage;
@@ -46,36 +49,35 @@
<refsynopsisdiv>
<cmdsynopsis>
<command>&dhpackage;</command>
- <arg choice="opt">Options</arg>
- <arg choice="opt">
+ <arg>
<replaceable>infile.fasta</replaceable>
</arg>
<arg choice="opt">
<replaceable>outfile.fasta</replaceable>
</arg>
+ <arg choice="opt">Options</arg>
</cmdsynopsis>
<cmdsynopsis>
<command>&dhpackage;</command>
- <arg choice="opt">Options</arg>
- <arg choice="opt"> -i
+ <arg> -i
<replaceable>infile.fasta</replaceable>
</arg>
<arg choice="opt"> -o
<replaceable>outfile.fasta</replaceable>
</arg>
+ <arg choice="opt">Options</arg>
</cmdsynopsis>
-
<cmdsynopsis>
<command>&dhpackage;</command>
- <arg choice="opt">Options</arg>
- <arg choice="opt"> <
+ <arg> <
<replaceable>infile.fasta</replaceable>
</arg>
<arg choice="opt"> >
<replaceable>outfile.fasta</replaceable>
</arg>
+ <arg choice="opt">Options</arg>
</cmdsynopsis>
</refsynopsisdiv>
@@ -88,48 +90,135 @@
</refsect1>
<refsect1>
<title>OPTIONS</title>
-
<variablelist>
<varlistentry>
- <term><option>-i</option>
- <option>-input</option>
+ <term>
+ <option>-s</option>
+ <option>-gpo</option>
+ <option>-gapopen</option>
+ <option>-gap_open</option>
+ <parameter>x</parameter>
</term>
<listitem>
- <para>Name of the input file in FASTA format.</para>
+ <para>Gap open penalty<!-- (default 6.0)-->.</para>
</listitem>
</varlistentry>
<varlistentry>
- <term><option>-o</option>
- <option>-output</option>
+ <term>
+ <option>-e</option>
+ <option>-gpe</option>
+ <option>-gap_ext</option>
+ <option>-gapextension</option>
+ <parameter>x</parameter>
</term>
<listitem>
- <para>Name of the output file (in FASTA format).</para>
+ <para>Gap extension penalty.</para>
</listitem>
</varlistentry>
<varlistentry>
<term>
- <option>-gpo</option>
- <option>-gap_open</option>
+ <option>-t</option>
+ <option>-tgpe</option>
+ <option>-terminal_gap_extension_penalty</option>
<parameter>x</parameter>
</term>
+ <listitem><para>Terminal gap penalties.</para></listitem>
+ </varlistentry>
+
+ <varlistentry>
+ <term>
+ <option>-m</option>
+ <option>-bonus</option>
+ <option>-matrix_bonus</option>
+ <parameter>x</parameter>
+ </term>
<listitem>
- <para>Gap open penalty (default 6.0).</para>
+ <para>A constant added to the substitution matrix.</para>
</listitem>
</varlistentry>
<varlistentry>
- <term><option>-gpe</option>
- <option>-gap_ext</option>
- <parameter>x</parameter>
+ <term>
+ <option>-c</option>
+ <option>-sort</option>
+ <parameter><input, tree, gaps.></parameter>
</term>
<listitem>
- <para>Gap extension penalty (default 0.9).</para>
+ <para>The order in which the sequences appear in the output alignment.</para>
</listitem>
</varlistentry>
<varlistentry>
+ <term>
+ <option>-g</option>
+ <option>-feature</option>
+ </term>
+ <listitem>
+ <para>
+ Selects feature mode and specifies which features are to be used: e.g. all, maxplp, STRUCT, PFAM-A....
+ </para>
+ </listitem>
+ </varlistentry>
+
+ <varlistentry>
+ <term>
+ <option>-d</option>
+ <option>-distance</option>
+ <parameter><wu, pair></parameter>
+ </term>
+ <listitem><para>Distance method</para></listitem>
+ </varlistentry>
+
+ <varlistentry>
+ <term>
+ <option>-b</option>
+ <option>-tree</option>
+ <option>-guide-tree</option>
+ <parameter><nj, upgma></parameter>
+ </term>
+ <listitem>
+ <para>Guide tree method.</para>
+ </listitem>
+ </varlistentry>
+
+ <varlistentry>
+ <term>
+ <option>-z</option>
+ <option>-zcutoff</option>
+ </term>
+ <listitem>
+ <para>
+ Parameter used in the wu-manber based distance calculation.
+ </para>
+ </listitem>
+ </varlistentry>
+
+ <varlistentry>
+ <term>
+ <option>-i</option>
+ <option>-in</option>
+ <option>-input</option>
+ </term>
+ <listitem>
+ <para>Name of the input file.</para>
+ </listitem>
+ </varlistentry>
+
+ <varlistentry>
+ <term>
+ <option>-o</option>
+ <option>-out</option>
+ <option>-output</option>
+ </term>
+ <listitem>
+ <para>Name of the output file.</para>
+ </listitem>
+ </varlistentry>
+
+
+<!-- <varlistentry>
<term><option>-p</option>
<option>-points</option>
</term>
@@ -154,17 +243,31 @@
<para>Fast heuristic alignment ( recommended for >500 sequences)</para>
</listitem>
</varlistentry>
+-->
+
+ <varlistentry>
+ <term>
+ <option>-f</option>
+ <option>-format</option>
+ <parameter><fasta, msf, aln, clu, macsim></parameter>
+ </term>
+ <listitem>
+ <para>The output format.</para>
+ </listitem>
+ </varlistentry>
<varlistentry>
- <term><option>-q</option>
+ <term>
+ <option>-q</option>
+ <option>-quiet</option>
</term>
<listitem>
- <para><quote>quiet</quote> - no messages are sent to standard error.</para>
+ <para>Print nothing to STDERR. Read nothing from STDIN.</para>
</listitem>
</varlistentry>
</variablelist>
- <para> In default mode Kalign will use the Wu-Manber algorithm for distance calculation only. (recommended for < 500 sequences)</para>
+<!-- <para> In default mode Kalign will use the Wu-Manber algorithm for distance calculation only. (recommended for < 500 sequences)</para>-->
</refsect1>
<refsect1>
@@ -177,7 +280,7 @@
<refsect1>
<title>COPYRIGHTS</title>
- <para>Copyright (C) 2004, 2005, 2006 Timo Lassmann <email>timo.lassmann at cgb.ki.se</email>. Kalign is free software. You can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation.</para>
+ <para>Copyright (C) 2004, 2005, 2006 Timo Lassmann <email>timolassmann at gmail.com</email>. Kalign is free software. You can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation.</para>
<para>This manual page was written by &dhusername; &dhemail; for
the &debian; system (but may be used by others). Permission is
Deleted: trunk/packages/kalign/trunk/debian/manpages
===================================================================
--- trunk/packages/kalign/trunk/debian/manpages 2007-02-17 09:25:42 UTC (rev 213)
+++ trunk/packages/kalign/trunk/debian/manpages 2007-02-19 12:48:33 UTC (rev 214)
@@ -1 +0,0 @@
-debian/kalign.1
Modified: trunk/packages/kalign/trunk/debian/rules
===================================================================
--- trunk/packages/kalign/trunk/debian/rules 2007-02-17 09:25:42 UTC (rev 213)
+++ trunk/packages/kalign/trunk/debian/rules 2007-02-19 12:48:33 UTC (rev 214)
@@ -5,7 +5,7 @@
# As a special exception, when this file is copied by dh-make into a
# dh-make output file, you may use that output file without restriction.
# This special exception was added by Craig Small in version 0.37 of dh-make.
-# Modifications by Charles Plessy during the year 2006
+# Modifications by Charles Plessy during the years 2006 and 2007
# are hereby released as "public domain".
CFLAGS = -Wall -g
@@ -18,6 +18,7 @@
build:
dh_testdir
+ ./configure
$(MAKE)
xsltproc -o debian/ -''-nonet /usr/share/xml/docbook/stylesheet/nwalsh/manpages/docbook.xsl debian/kalign.1.xml
touch build-stamp
@@ -42,8 +43,8 @@
dh_testdir
dh_testroot
dh_installchangelogs
- dh_installdocs
- dh_installman
+ dh_installdocs README
+ dh_installman debian/kalign.1
dh_link
dh_strip
dh_compress
Modified: trunk/packages/kalign/trunk/debian/watch
===================================================================
--- trunk/packages/kalign/trunk/debian/watch 2007-02-17 09:25:42 UTC (rev 213)
+++ trunk/packages/kalign/trunk/debian/watch 2007-02-19 12:48:33 UTC (rev 214)
@@ -1,2 +1,2 @@
version=3
-http://msa.cgb.ki.se/downloads/ kalign-(\d).(\d+).tgz
+http://msa.cgb.ki.se/downloads/ kalign-?(\d).(\d+).tgz
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