[med-svn] r4174 - trunk/packages/kalign/trunk/debian
Andreas Tille
tille at alioth.debian.org
Tue Oct 6 14:44:38 UTC 2009
Author: tille
Date: 2009-10-06 14:44:38 +0000 (Tue, 06 Oct 2009)
New Revision: 4174
Added:
trunk/packages/kalign/trunk/debian/docs
trunk/packages/kalign/trunk/debian/install
trunk/packages/kalign/trunk/debian/manpages
Removed:
trunk/packages/kalign/trunk/debian/kalign.1.xml
Modified:
trunk/packages/kalign/trunk/debian/changelog
trunk/packages/kalign/trunk/debian/control
trunk/packages/kalign/trunk/debian/rules
Log:
Clean up packaging, short debian/rules file
Modified: trunk/packages/kalign/trunk/debian/changelog
===================================================================
--- trunk/packages/kalign/trunk/debian/changelog 2009-10-06 13:06:07 UTC (rev 4173)
+++ trunk/packages/kalign/trunk/debian/changelog 2009-10-06 14:44:38 UTC (rev 4174)
@@ -1,9 +1,22 @@
kalign (2.04-2) UNRELEASED; urgency=low
+ [ David Paleino ]
* Removed myself from Uploaders
- -- David Paleino <d.paleino at gmail.com> Sat, 23 May 2009 14:45:04 +0200
+ [ Andreas Tille ]
+ * debian/control:
+ - Standards-Version: 3.8.3
+ - debhelper (>= 7.1) to use override facility
+ * debian/rules:
+ - removed code to create manpage - just keep the created one
+ - short rules file using dh
+ * debian/watch:
+ - deactivated; upstream does not seem to respond to our request
+ to enable versioned tarballs - so the watch file makes no sense
+ Closes: #456479
+ -- Andreas Tille <tille at debian.org> Tue, 06 Oct 2009 16:21:45 +0200
+
kalign (2.04-1) unstable; urgency=low
* New upstream release.
Modified: trunk/packages/kalign/trunk/debian/control
===================================================================
--- trunk/packages/kalign/trunk/debian/control 2009-10-06 13:06:07 UTC (rev 4173)
+++ trunk/packages/kalign/trunk/debian/control 2009-10-06 14:44:38 UTC (rev 4174)
@@ -1,12 +1,12 @@
Source: kalign
Section: science
Priority: optional
-Maintainer: Debian-Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
DM-Upload-Allowed: yes
Uploaders: Charles Plessy <plessy at debian.org>,
Andreas Tille <tille at debian.org>
-Build-Depends: debhelper (>= 7)
-Standards-Version: 3.8.0
+Build-Depends: debhelper (>= 7.1)
+Standards-Version: 3.8.3
Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/kalign/trunk/?rev=0&sc=0
Vcs-Svn: svn://svn.debian.org/svn/debian-med/trunk/packages/kalign/trunk/
Homepage: http://msa.cgb.ki.se
Added: trunk/packages/kalign/trunk/debian/docs
===================================================================
--- trunk/packages/kalign/trunk/debian/docs (rev 0)
+++ trunk/packages/kalign/trunk/debian/docs 2009-10-06 14:44:38 UTC (rev 4174)
@@ -0,0 +1 @@
+README
Added: trunk/packages/kalign/trunk/debian/install
===================================================================
--- trunk/packages/kalign/trunk/debian/install (rev 0)
+++ trunk/packages/kalign/trunk/debian/install 2009-10-06 14:44:38 UTC (rev 4174)
@@ -0,0 +1 @@
+kalign usr/bin
Deleted: trunk/packages/kalign/trunk/debian/kalign.1.xml
===================================================================
--- trunk/packages/kalign/trunk/debian/kalign.1.xml 2009-10-06 13:06:07 UTC (rev 4173)
+++ trunk/packages/kalign/trunk/debian/kalign.1.xml 2009-10-06 14:44:38 UTC (rev 4174)
@@ -1,344 +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 V4.5//EN"
-"/usr/share/xml/docbook/schema/dtd/4.5/docbookx.dtd" [
- <!ENTITY dhfirstname "<firstname>Charles</firstname>">
- <!ENTITY dhsurname "<surname>Plessy</surname>">
- <!ENTITY dhdate "February 25, 2009">
- <!ENTITY dhsection "<manvolnum>1</manvolnum>">
- <!ENTITY dhemail "<email>plessy at debian.org</email>">
- <!ENTITY dhusername "Charles Plessy">
- <!ENTITY dhucpackage "<refentrytitle>KALIGN</refentrytitle>">
- <!ENTITY dhpackage "kalign">
- <!ENTITY dhrelease "2.04">
- <!ENTITY dhtitle "Kalign User Manual">
- <!ENTITY debian "<productname>Debian</productname>">
- <!ENTITY gnu "<acronym>GNU</acronym>">
- <!ENTITY gpl "&gnu; <acronym>GPL</acronym>">
-]>
-
-<!-- Copyright 2006?2009 Charles Plessy. You can use, copy, and redistribute this manpage under the same terms as kalign itself. -->
-
-<refentry>
- <refentryinfo>
- <title>&dhtitle;</title>
- <productname>&dhpackage;</productname>
- <releaseinfo role="version">&dhrelease;</releaseinfo>
- <date>&dhdate;</date>
- <authorgroup>
- <author>
- <firstname>Timo</firstname>
- <surname>Lassmann</surname>
- <contrib>Upstream author of Kalign.</contrib>
- <address>
- <email>timolassmann at gmail.com</email>
- </address>
- </author>
- <author>
- &dhfirstname;
- &dhsurname;
- <contrib>Wrote the manpage.</contrib>
- <address>&dhemail;</address>
- </author>
- </authorgroup>
- <copyright>
- <year>2004</year>
- <year>2005</year>
- <year>2006</year>
- <year>2007</year>
- <year>2008</year>
- <holder>Timo Lassmann</holder>
- </copyright>
- <legalnotice>
- <para>
- 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 same terms as kalign itself.
- </para>
- <para>
- On Debian systems, the complete text of the GNU General Public License version 2 can be found in <filename>/usr/share/common-licenses/GPL-2</filename>.
- </para>
- </legalnotice>
- </refentryinfo>
- <refmeta>
- &dhucpackage;
-
- &dhsection;
- </refmeta>
- <refnamediv>
- <refname>&dhpackage;</refname>
-
- <refpurpose>performs multiple alignment of biological sequences.</refpurpose>
- </refnamediv>
- <refsynopsisdiv>
- <cmdsynopsis>
- <command>&dhpackage;</command>
- <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> -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> <
- <replaceable>infile.fasta</replaceable>
- </arg>
- <arg choice="opt"> >
- <replaceable>outfile.fasta</replaceable>
- </arg>
- <arg choice="opt">Options</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 Muth?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.</para>
- </refsect1>
-
- <refsect1>
- <title>OPTIONS</title>
- <variablelist>
- <varlistentry>
- <term>
- <option>-s</option>
- <option>-gpo</option>
- <option>-gapopen</option>
- <option>-gap_open</option>
- <parameter>x</parameter>
- </term>
- <listitem>
- <para>Gap open penalty<!-- (default 6.0)-->.</para>
- </listitem>
- </varlistentry>
-
- <varlistentry>
- <term>
- <option>-e</option>
- <option>-gpe</option>
- <option>-gap_ext</option>
- <option>-gapextension</option>
- <parameter>x</parameter>
- </term>
- <listitem>
- <para>Gap extension penalty.</para>
- </listitem>
- </varlistentry>
-
- <varlistentry>
- <term>
- <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>A constant added to the substitution matrix.</para>
- </listitem>
- </varlistentry>
-
- <varlistentry>
- <term>
- <option>-c</option>
- <option>-sort</option>
- <parameter><input, tree, gaps.></parameter>
- </term>
- <listitem>
- <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>-same_feature_score</option>
- </term>
- <listitem>
- <para>
- Score for aligning same features.
- </para>
- </listitem>
- </varlistentry>
-
- <varlistentry>
- <term>
- <option>-diff_feature_score</option>
- </term>
- <listitem>
- <para>
- Penalty for aligning different features.
- </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>
- <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>-a</option>
- <option>-gap_inc</option>
- </term>
- <listitem>
- <para>Increases gap penalties depending on the number of existing gaps.</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>
- <option>-quiet</option>
- </term>
- <listitem>
- <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>-->
- </refsect1>
-
- <refsect1>
- <title>REFERENCES</title>
- <itemizedlist>
- <listitem>
- <para>
- Timo Lassmann and Erik L.L. Sonnhammer (2005) Kalign - an accurate and fast multiple sequence alignment algorithm. BMC Bioinformatics 6:298
- </para>
- </listitem>
- <listitem>
- <para>
- Timo Lassmann, Oliver Frings and Erik L. L. Sonnhammer (2009) Kalign2: high-performance multiple alignment of protein and nucleotide sequences allowing external features. Nucleic Acid Research 3:858?865.
- </para>
- </listitem>
- </itemizedlist>
- </refsect1>
-</refentry>
-
Added: trunk/packages/kalign/trunk/debian/manpages
===================================================================
--- trunk/packages/kalign/trunk/debian/manpages (rev 0)
+++ trunk/packages/kalign/trunk/debian/manpages 2009-10-06 14:44:38 UTC (rev 4174)
@@ -0,0 +1 @@
+debian/kalign.1
Modified: trunk/packages/kalign/trunk/debian/rules
===================================================================
--- trunk/packages/kalign/trunk/debian/rules 2009-10-06 13:06:07 UTC (rev 4173)
+++ trunk/packages/kalign/trunk/debian/rules 2009-10-06 14:44:38 UTC (rev 4174)
@@ -1,67 +1,9 @@
#!/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 years 2006 and 2007
-# are hereby released as "public domain".
-CFLAGS = -Wall -g
+%:
+ dh $@
-ifneq (,$(findstring noopt,$(DEB_BUILD_OPTIONS)))
- CFLAGS += -O0
-else
- CFLAGS += -O2
-endif
-
-XP=xsltproc \
- -o debian/ \
- -''-nonet /usr/share/xml/docbook/stylesheet/nwalsh/manpages/docbook.xsl
-
-kalign.1: debian/kalign.1.xml
- $(XP) $<
-
-build: build-stamp
-build-stamp:
- dh_testdir
- ./configure
- $(MAKE)
- touch $@
-
-clean:
- -rm build-stamp
- dh_testdir
- dh_testroot
- rm -f build-stamp configure-stamp
- [ ! -f Makefile ] || $(MAKE) clean
- dh_clean
-
-install: build
- dh_testdir
- dh_testroot
- dh_prep
- dh_installdirs /usr/bin
- install -o 755 kalign debian/kalign/usr/bin/
-
-binary-indep:
-
-binary-arch: build install
- dh_testdir
- dh_testroot
- dh_installchangelogs
- dh_installdocs README
- dh_installman debian/kalign.1
- 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
+override_dh_auto_install:
+ dh_install
More information about the debian-med-commit
mailing list