[med-svn] r31 - in trunk/packages/kalign/trunk: . debian
Charles Plessy
charles-guest at costa.debian.org
Sun Apr 30 11:48:35 UTC 2006
Author: charles-guest
Date: 2006-04-30 11:48:35 +0000 (Sun, 30 Apr 2006)
New Revision: 31
Added:
trunk/packages/kalign/trunk/debian/
trunk/packages/kalign/trunk/debian/changelog
trunk/packages/kalign/trunk/debian/compat
trunk/packages/kalign/trunk/debian/control
trunk/packages/kalign/trunk/debian/copyright
trunk/packages/kalign/trunk/debian/dirs
trunk/packages/kalign/trunk/debian/docs
trunk/packages/kalign/trunk/debian/kalign.1.xml
trunk/packages/kalign/trunk/debian/manpages
trunk/packages/kalign/trunk/debian/rules
trunk/packages/kalign/trunk/debian/watch
Modified:
trunk/packages/kalign/trunk/Makefile
Log:
Load kalign-1.04 into trunk/packages/kalign/trunk.
Property changes on: trunk/packages/kalign/trunk/Makefile
___________________________________________________________________
Name: svn:executable
-
+ *
Added: trunk/packages/kalign/trunk/debian/changelog
===================================================================
--- trunk/packages/kalign/trunk/debian/changelog 2006-04-30 11:46:08 UTC (rev 30)
+++ trunk/packages/kalign/trunk/debian/changelog 2006-04-30 11:48:35 UTC (rev 31)
@@ -0,0 +1,6 @@
+kalign (1.04-1) unstable; urgency=low
+
+ * Initial release Closes: #365344
+
+ -- Charles Plessy <charles-debian-nospam at plessy.org> Sat, 29 Apr 2006 23:02:57 +0900
+
Added: trunk/packages/kalign/trunk/debian/compat
===================================================================
--- trunk/packages/kalign/trunk/debian/compat 2006-04-30 11:46:08 UTC (rev 30)
+++ trunk/packages/kalign/trunk/debian/compat 2006-04-30 11:48:35 UTC (rev 31)
@@ -0,0 +1 @@
+4
Added: trunk/packages/kalign/trunk/debian/control
===================================================================
--- trunk/packages/kalign/trunk/debian/control 2006-04-30 11:46:08 UTC (rev 30)
+++ trunk/packages/kalign/trunk/debian/control 2006-04-30 11:48:35 UTC (rev 31)
@@ -0,0 +1,23 @@
+Source: kalign
+Section: science
+Priority: optional
+Maintainer: Charles Plessy <charles-debian-nospam at plessy.org>
+Build-Depends: debhelper (>= 4.0.0), xsltproc, docbook-xsl
+Standards-Version: 3.6.2
+
+Package: kalign
+Architecture: any
+Depends: ${shlibs:Depends}, ${misc:Depends}
+Description: Global and progressive multiple sequence alignment
+ Kalign is a command line tool to perform multiple alignment of
+ biological sequences. It employs the Wu-Manber string-matching
+ algorithm, to improve both the accuracy and speed of the alignment.
+ It uses global, progressive alignment approach, enriched by employing
+ an approximate string-matching algorithm to calculate sequence
+ distances and by incorporating local matches into the otherwise global
+ alignment. In comparisons made by its authors, Kalign was about 10
+ times faster than ClustalW and, depending on the alignment size, up to
+ 50 times faster than popular iterative methods. It has been published
+ in Lassmann and Sonnhammer, BMC Bioinformatics 2005, 6:298.
+ .
+ Homepage: http://msa.cgb.ki.se
Added: trunk/packages/kalign/trunk/debian/copyright
===================================================================
--- trunk/packages/kalign/trunk/debian/copyright 2006-04-30 11:46:08 UTC (rev 30)
+++ trunk/packages/kalign/trunk/debian/copyright 2006-04-30 11:48:35 UTC (rev 31)
@@ -0,0 +1,28 @@
+This package was debianized by Charles Plessy
+<charles-debian-nospam at plessy.org> on Sat, 29 Apr 2006. The packaging work is
+in the public domain unless stated otherwise. The manpage for kalign and its
+source are licenced under the GPL.
+
+It was downloaded from http://msa.cgb.ki.se/downloads/kalign-1.04.tgz
+
+Copyright (C) 2004, 2005, 2006 Timo Lassmann <timo.lassmann at cgb.ki.se>
+
+License:
+
+ This package 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; either version 2 of the License, or
+ (at your option) any later version.
+
+ This package is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ GNU General Public License for more details.
+
+ You should have received a copy of the GNU General Public License
+ along with this package; if not, write to the Free Software
+ Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA
+
+On Debian systems, the complete text of the GNU General
+Public License can be found in `/usr/share/common-licenses/GPL'.
+
Added: trunk/packages/kalign/trunk/debian/dirs
===================================================================
--- trunk/packages/kalign/trunk/debian/dirs 2006-04-30 11:46:08 UTC (rev 30)
+++ trunk/packages/kalign/trunk/debian/dirs 2006-04-30 11:48:35 UTC (rev 31)
@@ -0,0 +1 @@
+/usr/bin
Added: trunk/packages/kalign/trunk/debian/docs
===================================================================
--- trunk/packages/kalign/trunk/debian/docs 2006-04-30 11:46:08 UTC (rev 30)
+++ trunk/packages/kalign/trunk/debian/docs 2006-04-30 11:48:35 UTC (rev 31)
@@ -0,0 +1 @@
+README
Added: trunk/packages/kalign/trunk/debian/kalign.1.xml
===================================================================
--- trunk/packages/kalign/trunk/debian/kalign.1.xml 2006-04-30 11:46:08 UTC (rev 30)
+++ trunk/packages/kalign/trunk/debian/kalign.1.xml 2006-04-30 11:48:35 UTC (rev 31)
@@ -0,0 +1,196 @@
+<?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" [
+
+
+ <!ENTITY dhfirstname "<firstname>Charles</firstname>">
+ <!ENTITY dhsurname "<surname>Plessy</surname>">
+ <!ENTITY dhdate "<date>avril 29, 2006</date>">
+ <!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 debian "<productname>Debian</productname>">
+ <!ENTITY gnu "<acronym>GNU</acronym>">
+ <!ENTITY gpl "&gnu; <acronym>GPL</acronym>">
+]>
+
+<!-- Copyright 2006 Charles Plessy. You can use, copy, and redistribute this manpage under the GNU GPL. -->
+
+<refentry>
+ <refentryinfo>
+ <address>
+ &dhemail;
+ </address>
+<!-- <author>
+ &dhfirstname;
+ &dhsurname;
+ </author> -->
+ <copyright>
+ <year>2006</year>
+ <holder>&dhusername;</holder>
+ </copyright>
+ &dhdate;
+ </refentryinfo>
+ <refmeta>
+ &dhucpackage;
+
+ &dhsection;
+ </refmeta>
+ <refnamediv>
+ <refname>&dhpackage;</refname>
+
+ <refpurpose>performs multiple alignment of biological sequences.</refpurpose>
+ </refnamediv>
+ <refsynopsisdiv>
+ <cmdsynopsis>
+ <command>&dhpackage;</command>
+ <arg choice="opt">Options</arg>
+ <arg choice="opt">
+ <replaceable>infile.fasta</replaceable>
+ </arg>
+ <arg choice="opt">
+ <replaceable>outfile.fasta</replaceable>
+ </arg>
+ </cmdsynopsis>
+
+ <cmdsynopsis>
+ <command>&dhpackage;</command>
+ <arg choice="opt">Options</arg>
+ <arg choice="opt"> -i
+ <replaceable>infile.fasta</replaceable>
+ </arg>
+ <arg choice="opt"> -o
+ <replaceable>outfile.fasta</replaceable>
+ </arg>
+ </cmdsynopsis>
+
+
+ <cmdsynopsis>
+ <command>&dhpackage;</command>
+ <arg choice="opt">Options</arg>
+ <arg choice="opt"> <
+ <replaceable>infile.fasta</replaceable>
+ </arg>
+ <arg choice="opt"> >
+ <replaceable>outfile.fasta</replaceable>
+ </arg>
+ </cmdsynopsis>
+
+ </refsynopsisdiv>
+ <refsect1>
+ <title>DESCRIPTION</title>
+
+ <para><command>Kalign</command> is a command line tool to perform multiple alignment of biological sequences. It employs the Wu-Manber string-matching algorithm, to improve both the accuracy and speed of the alignment. It uses global, progressive alignment approach, enriched by employing an approximate string-matching algorithm to calculate sequence distances and by incorporating local matches into the otherwise global alignment. In comparisons made by its authors, Kalign was about 10 times faster than ClustalW and, depending on the alignment size, up to 50 times faster than popular iterative methods.</para>
+
+
+ </refsect1>
+ <refsect1>
+ <title>OPTIONS</title>
+
+ <variablelist>
+ <varlistentry>
+ <term><option>-i</option>
+ <option>-input</option>
+ </term>
+ <listitem>
+ <para>Name of the input file in FASTA format.</para>
+ </listitem>
+ </varlistentry>
+
+ <varlistentry>
+ <term><option>-o</option>
+ <option>-output</option>
+ </term>
+ <listitem>
+ <para>Name of the output file (in FASTA format).</para>
+ </listitem>
+ </varlistentry>
+
+ <varlistentry>
+ <term>
+ <option>-gpo</option>
+ <option>-gap_open</option>
+ <parameter>x</parameter>
+ </term>
+ <listitem>
+ <para>Gap open penalty (default 6.0).</para>
+ </listitem>
+ </varlistentry>
+
+ <varlistentry>
+ <term><option>-gpe</option>
+ <option>-gap_ext</option>
+ <parameter>x</parameter>
+ </term>
+ <listitem>
+ <para>Gap extension penalty (default 0.9).</para>
+ </listitem>
+ </varlistentry>
+
+ <varlistentry>
+ <term><option>-p</option>
+ <option>-points</option>
+ </term>
+ <listitem>
+ <para>Wu-Manber algorithm used in both distance calculation and dynamic programming.</para>
+ </listitem>
+ </varlistentry>
+
+ <varlistentry>
+ <term><option>-w</option>
+ </term>
+ <listitem>
+ <para>Wu-Manber algorithm will not be used at all.</para>
+ </listitem>
+ </varlistentry>
+
+ <varlistentry>
+ <term><option>-f</option>
+ <option>-fast</option>
+ </term>
+ <listitem>
+ <para>Fast heuristic alignment ( recommended for >500 sequences)</para>
+ </listitem>
+ </varlistentry>
+
+ <varlistentry>
+ <term><option>-q</option>
+ </term>
+ <listitem>
+ <para><quote>quiet</quote> - no messages are sent to standard error.</para>
+ </listitem>
+ </varlistentry>
+ </variablelist>
+
+ <para> In default mode Kalign will use the Wu-Manber algorithm for distance calculation only. (recommended for < 500 sequences)</para>
+ </refsect1>
+
+ <refsect1>
+ <title>REFERENCE</title>
+ <para>
+ Please cite Timo Lassmann and Erik L.L. Sonnhammer (2005) Kalign - an accurate and fast multiple sequence alignment algorithm. BMC Bioinformatics 6:298
+ </para>
+ </refsect1>
+
+ <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>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>
+
+ <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>
+
Added: trunk/packages/kalign/trunk/debian/manpages
===================================================================
--- trunk/packages/kalign/trunk/debian/manpages 2006-04-30 11:46:08 UTC (rev 30)
+++ trunk/packages/kalign/trunk/debian/manpages 2006-04-30 11:48:35 UTC (rev 31)
@@ -0,0 +1 @@
+debian/kalign.1
Added: trunk/packages/kalign/trunk/debian/rules
===================================================================
--- trunk/packages/kalign/trunk/debian/rules 2006-04-30 11:46:08 UTC (rev 30)
+++ trunk/packages/kalign/trunk/debian/rules 2006-04-30 11:48:35 UTC (rev 31)
@@ -0,0 +1,58 @@
+#!/usr/bin/make -f
+# -*- makefile -*-
+# Build rules for the Debian package kalign
+# This file was originally written by Joey Hess and Craig Small.
+# 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
+# are hereby released as "public domain".
+
+CFLAGS = -Wall -g
+
+ifneq (,$(findstring noopt,$(DEB_BUILD_OPTIONS)))
+ CFLAGS += -O0
+else
+ CFLAGS += -O2
+endif
+
+build:
+ dh_testdir
+ $(MAKE)
+ xsltproc -o debian/ -''-nonet /usr/share/sgml/docbook/stylesheet/xsl/nwalsh/manpages/docbook.xsl debian/kalign.1.xml
+ touch build-stamp
+
+clean:
+ dh_testdir
+ dh_testroot
+ rm -f build-stamp configure-stamp
+ -$(MAKE) clean
+ dh_clean debian/kalign.1
+
+install: build
+ dh_testdir
+ dh_testroot
+ dh_clean -k
+ dh_installdirs
+ install -o 755 kalign debian/kalign/usr/bin/
+
+binary-indep: build install
+
+binary-arch: build install
+ dh_testdir
+ dh_testroot
+ dh_installchangelogs
+ dh_installdocs
+ dh_installman
+ dh_link
+ dh_strip
+ dh_compress
+ dh_fixperms
+ dh_installdeb
+ dh_shlibdeps
+ dh_gencontrol
+ dh_md5sums
+ dh_builddeb
+
+binary: binary-indep binary-arch
+.PHONY: build clean binary-indep binary-arch binary install configure
Property changes on: trunk/packages/kalign/trunk/debian/rules
___________________________________________________________________
Name: svn:executable
+ *
Added: trunk/packages/kalign/trunk/debian/watch
===================================================================
--- trunk/packages/kalign/trunk/debian/watch 2006-04-30 11:46:08 UTC (rev 30)
+++ trunk/packages/kalign/trunk/debian/watch 2006-04-30 11:48:35 UTC (rev 31)
@@ -0,0 +1,2 @@
+version=3
+http://msa.cgb.ki.se/downloads/kalign-(.*)\.tar\.gz
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