[med-svn] r3140 - trunk/packages/kalign/trunk/debian
plessy at alioth.debian.org
plessy at alioth.debian.org
Wed Feb 25 15:26:43 UTC 2009
Author: plessy
Date: 2009-02-25 15:26:43 +0000 (Wed, 25 Feb 2009)
New Revision: 3140
Added:
trunk/packages/kalign/trunk/debian/reference
Modified:
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/kalign.1
trunk/packages/kalign/trunk/debian/kalign.1.xml
trunk/packages/kalign/trunk/debian/rules
Log:
New upstream release and routine work.
* New upstream release.
* debian/copyright made machine-readable.
* debian/rules: replaced deprecated dh_clean -k by dh_prep.
* debian/control:
- Updated my email address (debian/control).
- Checked compliance with Policy 3.8.0 (no changes needed).
- Using debhelper 7 (also in debian/compat).
- Upadated description and moved reference to debian/reference.
* debian/kalign.1*: updated the manual pages.
Modified: trunk/packages/kalign/trunk/debian/changelog
===================================================================
--- trunk/packages/kalign/trunk/debian/changelog 2009-02-25 13:45:27 UTC (rev 3139)
+++ trunk/packages/kalign/trunk/debian/changelog 2009-02-25 15:26:43 UTC (rev 3140)
@@ -1,8 +1,16 @@
-kalign (2.03-3) UNRELEASED; urgency=low
+kalign (2.04-1) unstable; urgency=low
- * Updated my email address.
+ * New upstream release.
+ * debian/copyright made machine-readable.
+ * debian/rules: replaced deprecated dh_clean -k by dh_prep.
+ * debian/control:
+ - Updated my email address (debian/control).
+ - Checked compliance with Policy 3.8.0 (no changes needed).
+ - Using debhelper 7 (also in debian/compat).
+ - Upadated description and moved reference to debian/reference.
+ * debian/kalign.1*: updated the manual pages.
- -- Charles Plessy <plessy at debian.org> Sun, 27 Apr 2008 17:03:10 +0900
+ -- Charles Plessy <plessy at debian.org> Thu, 26 Feb 2009 00:19:44 +0900
kalign (2.03-2) unstable; urgency=low
Modified: trunk/packages/kalign/trunk/debian/compat
===================================================================
--- trunk/packages/kalign/trunk/debian/compat 2009-02-25 13:45:27 UTC (rev 3139)
+++ trunk/packages/kalign/trunk/debian/compat 2009-02-25 15:26:43 UTC (rev 3140)
@@ -1 +1 @@
-5
+7
Modified: trunk/packages/kalign/trunk/debian/control
===================================================================
--- trunk/packages/kalign/trunk/debian/control 2009-02-25 13:45:27 UTC (rev 3139)
+++ trunk/packages/kalign/trunk/debian/control 2009-02-25 15:26:43 UTC (rev 3140)
@@ -6,8 +6,8 @@
Uploaders: Charles Plessy <plessy at debian.org>,
David Paleino <d.paleino at gmail.com>,
Andreas Tille <tille at debian.org>
-Build-Depends: debhelper (>= 5)
-Standards-Version: 3.7.3
+Build-Depends: debhelper (>= 7)
+Standards-Version: 3.8.0
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
@@ -18,12 +18,9 @@
Enhances: t-coffee
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
+ 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. 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.
+ alignment.
Modified: trunk/packages/kalign/trunk/debian/copyright
===================================================================
--- trunk/packages/kalign/trunk/debian/copyright 2009-02-25 13:45:27 UTC (rev 3139)
+++ trunk/packages/kalign/trunk/debian/copyright 2009-02-25 15:26:43 UTC (rev 3140)
@@ -1,27 +1,47 @@
-Copyright (C) 2004, 2005, 2006 Timo Lassmann <timolassmann at gmail.com>
+Format-Specification: http://wiki.debian.org/Proposals/CopyrightFormat?action=recall&rev=440
+Upstream-Name: Kalign
+Upstream-Maintainer: Timo Lassmann <timolassmann at gmail.com>
+Upstream-Source: http://msa.cgb.ki.se/downloads/kalign/current.tar.gz
-License:
+Files : *
+Copyright: © 2004–2008 Timo Lassmann <timolassmann at gmail.com>
+License: GPL-2+
+ 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
+X-Debian-Comment: On Debian systems, the complete text of the GNU General
+ Public License version 2 can be found in `/usr/share/common-licenses/GPL-2'.
- 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.
+Files: COPYING
+Copyright: © 1989, 1991 Free Software Foundation, Inc.
+License: changing it is not allowed.
+ Everyone is permitted to copy and distribute verbatim copies
+ of this license document, but changing it is not allowed.
- 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.
+Files: configure
+Copyright: © 2003 Free Software Foundation, Inc.
+License: unlimited permission to copy, distribute and modify it.
+ This configure script is free software; the Free Software Foundation
+ gives unlimited permission to copy, distribute and modify it.
- 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
+Files: debian/*
+Copyright: © 2006–2009 Charles Plessy <plessy at debian.org>
+ © 2008 David Paleino <d.paleino at gmail.com>
+ © 2008 Andreas Tille <tille at debian.org>
+Licence: As if in public domain.
+ The packaging work is in the public domain unless stated otherwise.
-On Debian systems, the complete text of the GNU General
-Public License can be found in `/usr/share/common-licenses/GPL'.
-
-Kalign was downloaded from http://msa.cgb.ki.se/
-
-This package was created 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 same
-licence as kalign itself.
+Files: debian/kalign.1*
+Copyright: © 2006–2009 Charles Plessy <plessy at debian.org>
+License: Same as kalign.
+ (See above)
Modified: trunk/packages/kalign/trunk/debian/kalign.1
===================================================================
--- trunk/packages/kalign/trunk/debian/kalign.1 2009-02-25 13:45:27 UTC (rev 3139)
+++ trunk/packages/kalign/trunk/debian/kalign.1 2009-02-25 15:26:43 UTC (rev 3140)
@@ -1,61 +1,71 @@
.\" Title: KALIGN
.\" Author: Timo Lassmann <timolassmann at gmail.com>
.\" Generator: DocBook XSL Stylesheets v1.73.2 <http://docbook.sf.net/>
-.\" Date: February 17, 2007
+.\" Date: February 25, 2009
.\" Manual: Kalign User Manual
-.\" Source: kalign 2.03
+.\" Source: kalign 2.04
.\"
-.TH "KALIGN" "1" "February 17, 2007" "kalign 2.03" "Kalign User Manual"
+.TH "KALIGN" "1" "February 25, 2009" "kalign 2.04" "Kalign User Manual"
.\" disable hyphenation
.nh
.\" disable justification (adjust text to left margin only)
.ad l
.SH "NAME"
-kalign - performs multiple alignment of biological sequences.
+kalign \- performs multiple alignment of biological sequences.
.SH "SYNOPSIS"
.HP 7
-\fBkalign\fR [\fIinfile\.fasta\fR] [\fIoutfile\.fasta\fR] [Options]
+\fBkalign\fR [\fIinfile\&.fasta\fR] [\fIoutfile\&.fasta\fR] [Options]
.HP 7
-\fBkalign\fR [\-i\ \fIinfile\.fasta\fR] [\-o\ \fIoutfile\.fasta\fR] [Options]
+\fBkalign\fR [\-i\ \fIinfile\&.fasta\fR] [\-o\ \fIoutfile\&.fasta\fR] [Options]
.HP 7
-\fBkalign\fR [<\ \fIinfile\.fasta\fR] [>\ \fIoutfile\.fasta\fR] [Options]
+\fBkalign\fR [<\ \fIinfile\&.fasta\fR] [>\ \fIoutfile\&.fasta\fR] [Options]
.SH "DESCRIPTION"
.PP
\fBKalign\fR
-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\.
+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\&.
.SH "OPTIONS"
.PP
\fB\-s\fR \fB\-gpo\fR \fB\-gapopen\fR \fB\-gap_open\fR \fIx\fR
.RS 4
Gap open penalty
-\.
+\&.
.RE
.PP
\fB\-e\fR \fB\-gpe\fR \fB\-gap_ext\fR \fB\-gapextension\fR \fIx\fR
.RS 4
-Gap extension penalty\.
+Gap extension penalty\&.
.RE
.PP
\fB\-t\fR \fB\-tgpe\fR \fB\-terminal_gap_extension_penalty\fR \fIx\fR
.RS 4
-Terminal gap penalties\.
+Terminal gap penalties\&.
.RE
.PP
\fB\-m\fR \fB\-bonus\fR \fB\-matrix_bonus\fR \fIx\fR
.RS 4
-A constant added to the substitution matrix\.
+A constant added to the substitution matrix\&.
.RE
.PP
-\fB\-c\fR \fB\-sort\fR \fI<input, tree, gaps\.>\fR
+\fB\-c\fR \fB\-sort\fR \fI<input, tree, gaps\&.>\fR
.RS 4
-The order in which the sequences appear in the output alignment\.
+The order in which the sequences appear in the output alignment\&.
.RE
.PP
\fB\-g\fR \fB\-feature\fR
.RS 4
-Selects feature mode and specifies which features are to be used: e\.g\. all, maxplp, STRUCT, PFAM\-A\.\.\.\.
+Selects feature mode and specifies which features are to be used: e\&.g\&. all, maxplp, STRUCT, PFAM\-A?
.RE
.PP
+\fB\-same_feature_score\fR
+.RS 4
+Score for aligning same features\&.
+.RE
+.PP
+\fB\-diff_feature_score\fR
+.RS 4
+Penalty for aligning different features\&.
+.RE
+.PP
\fB\-d\fR \fB\-distance\fR \fI<wu, pair>\fR
.RS 4
Distance method
@@ -63,59 +73,70 @@
.PP
\fB\-b\fR \fB\-tree\fR \fB\-guide\-tree\fR \fI<nj, upgma>\fR
.RS 4
-Guide tree method\.
+Guide tree method\&.
.RE
.PP
\fB\-z\fR \fB\-zcutoff\fR
.RS 4
-Parameter used in the wu\-manber based distance calculation\.
+Parameter used in the wu\-manber based distance calculation\&.
.RE
.PP
\fB\-i\fR \fB\-in\fR \fB\-input\fR
.RS 4
-Name of the input file\.
+Name of the input file\&.
.RE
.PP
\fB\-o\fR \fB\-out\fR \fB\-output\fR
.RS 4
-Name of the output file\.
+Name of the output file\&.
.RE
.PP
+\fB\-a\fR \fB\-gap_inc\fR
+.RS 4
+Increases gap penalties depending on the number of existing gaps\&.
+.RE
+.PP
\fB\-f\fR \fB\-format\fR \fI<fasta, msf, aln, clu, macsim>\fR
.RS 4
-The output format\.
+The output format\&.
.RE
.PP
\fB\-q\fR \fB\-quiet\fR
.RS 4
-Print nothing to STDERR\. Read nothing from STDIN\.
+Print nothing to STDERR\&. Read nothing from STDIN\&.
.RE
-.SH "REFERENCE"
-.PP
-Please cite Timo Lassmann and Erik L\.L\. Sonnhammer (2005) Kalign \- an accurate and fast multiple sequence alignment algorithm\. BMC Bioinformatics 6:298
+.SH "REFERENCES"
+.sp
+.RS 4
+\h'-04'\(bu\h'+03'Timo Lassmann and Erik L\&.L\&. Sonnhammer (2005) Kalign \- an accurate and fast multiple sequence alignment algorithm\&. BMC Bioinformatics 6:298
+.RE
+.sp
+.RS 4
+\h'-04'\(bu\h'+03'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\&.
+.RE
.SH "AUTHORS"
.PP
-\fBTimo Lassmann\fR <\&timolassmann at gmail\.com\&>
+\fBTimo Lassmann\fR <\&timolassmann at gmail\&.com\&>
.sp -1n
.IP "" 4
-Upstream author of kalign\.
+Upstream author of Kalign\&.
.PP
-\fBCharles Plessy\fR <\&charles\-debian\-nospam at plessy\.org\&>
+\fBCharles Plessy\fR <\&plessy at debian\&.org\&>
.sp -1n
.IP "" 4
-Wrote the manpage\.
+Wrote the manpage\&.
.SH "COPYRIGHT"
-Copyright \(co 2004, 2005, 2006 Timo Lassmann
+Copyright \(co 2004, 2005, 2006, 2007, 2008 Timo Lassmann
.br
.PP
-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\.
+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\&.
.PP
This manual page was written by Charles Plessy
-<charles\-debian\-nospam at plessy\.org>
+<plessy at debian\&.org>
for the
Debian(TM)
-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\.
+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\&.
.PP
-On Debian systems, the complete text of the GNU General Public License can be found in
-\fI/usr/share/common\-licenses/GPL\fR\.
+On Debian systems, the complete text of the GNU General Public License version 2 can be found in
+\fI/usr/share/common\-licenses/GPL\-2\fR\&.
.sp
Modified: trunk/packages/kalign/trunk/debian/kalign.1.xml
===================================================================
--- trunk/packages/kalign/trunk/debian/kalign.1.xml 2009-02-25 13:45:27 UTC (rev 3139)
+++ trunk/packages/kalign/trunk/debian/kalign.1.xml 2009-02-25 15:26:43 UTC (rev 3140)
@@ -1,22 +1,24 @@
-<?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" [
+<?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 17, 2007">
+ <!ENTITY dhdate "February 25, 2009">
<!ENTITY dhsection "<manvolnum>1</manvolnum>">
- <!ENTITY dhemail "<email>charles-debian-nospam at plessy.org</email>">
+ <!ENTITY dhemail "<email>plessy at debian.org</email>">
<!ENTITY dhusername "Charles Plessy">
<!ENTITY dhucpackage "<refentrytitle>KALIGN</refentrytitle>">
<!ENTITY dhpackage "kalign">
- <!ENTITY dhrelease "2.03">
+ <!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 Charles Plessy. You can use, copy, and redistribute this manpage under the same terms as kalign itself. -->
+<!-- Copyright 2006?2009 Charles Plessy. You can use, copy, and redistribute this manpage under the same terms as kalign itself. -->
<refentry>
<refentryinfo>
@@ -28,7 +30,7 @@
<author>
<firstname>Timo</firstname>
<surname>Lassmann</surname>
- <contrib>Upstream author of kalign.</contrib>
+ <contrib>Upstream author of Kalign.</contrib>
<address>
<email>timolassmann at gmail.com</email>
</address>
@@ -44,6 +46,8 @@
<year>2004</year>
<year>2005</year>
<year>2006</year>
+ <year>2007</year>
+ <year>2008</year>
<holder>Timo Lassmann</holder>
</copyright>
<legalnotice>
@@ -54,7 +58,7 @@
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 can be found in <filename>/usr/share/common-licenses/GPL</filename>.
+ 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>
@@ -105,11 +109,9 @@
</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>
-
-
+ <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>
@@ -179,13 +181,35 @@
</term>
<listitem>
<para>
- Selects feature mode and specifies which features are to be used: e.g. all, maxplp, STRUCT, PFAM-A....
+ 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>
@@ -266,9 +290,18 @@
</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>
@@ -293,10 +326,19 @@
</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>
+ <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/reference
===================================================================
--- trunk/packages/kalign/trunk/debian/reference (rev 0)
+++ trunk/packages/kalign/trunk/debian/reference 2009-02-25 15:26:43 UTC (rev 3140)
@@ -0,0 +1,25 @@
+ at article{TimoLassmann02012009,
+author = {Lassmann, Timo and Frings, Oliver and Sonnhammer, Erik L. L.},
+title = {{Kalign2: high-performance multiple alignment of protein and nucleotide sequences allowing external features}},
+journal = {Nucl. Acids Res.},
+volume = {37},
+number = {3},
+pages = {858-865},
+doi = {10.1093/nar/gkn1006},
+year = {2009},
+URL = {http://nar.oxfordjournals.org/cgi/content/abstract/37/3/858},
+eprint = {http://nar.oxfordjournals.org/cgi/reprint/37/3/858.pdf}
+}
+ at Article{16343337,
+AUTHOR = {Lassmann, Timo and Sonnhammer, Erik},
+TITLE = {Kalign - an accurate and fast multiple sequence alignment algorithm},
+JOURNAL = {BMC Bioinformatics},
+VOLUME = {6},
+YEAR = {2005},
+NUMBER = {1},
+PAGES = {298},
+URL = {http://www.biomedcentral.com/1471-2105/6/298},
+DOI = {10.1186/1471-2105-6-298},
+PubMedID = {16343337},
+ISSN = {1471-2105},
+}
Modified: trunk/packages/kalign/trunk/debian/rules
===================================================================
--- trunk/packages/kalign/trunk/debian/rules 2009-02-25 13:45:27 UTC (rev 3139)
+++ trunk/packages/kalign/trunk/debian/rules 2009-02-25 15:26:43 UTC (rev 3140)
@@ -41,7 +41,7 @@
install: build
dh_testdir
dh_testroot
- dh_clean -k
+ dh_prep
dh_installdirs /usr/bin
install -o 755 kalign debian/kalign/usr/bin/
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