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 <[email protected]> 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 <[email protected]> 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 <[email protected]> +Maintainer: Debian Med Packaging Team <[email protected]> DM-Upload-Allowed: yes Uploaders: Charles Plessy <[email protected]>, Andreas Tille <[email protected]> -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>[email protected]</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>[email protected]</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 _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/mailman/listinfo/debian-med-commit
