[med-svn] r830 - trunk/packages/mafft/trunk/debian

hanska-guest at alioth.debian.org hanska-guest at alioth.debian.org
Sun Nov 18 10:14:01 UTC 2007 

Author: hanska-guest
Date: 2007-11-18 10:14:01 +0000 (Sun, 18 Nov 2007)
New Revision: 830

Added:
   trunk/packages/mafft/trunk/debian/mafft-homologs.1
   trunk/packages/mafft/trunk/debian/mafft.1
Modified:
   trunk/packages/mafft/trunk/debian/changelog
   trunk/packages/mafft/trunk/debian/control
   trunk/packages/mafft/trunk/debian/rules
Log:
* debian/mafft.1, debian/mafft-homologs.1 added - manpages built statically.
* debian/control:
  - B-D updated (see above)
  - added myself to Uploaders
  - moved XS-Vcs-* fields to Vcs-*
* debian/rules:
  - reflecting static build of manpages
  - minor changes

Modified: trunk/packages/mafft/trunk/debian/changelog
===================================================================
--- trunk/packages/mafft/trunk/debian/changelog	2007-11-18 10:07:41 UTC (rev 829)
+++ trunk/packages/mafft/trunk/debian/changelog	2007-11-18 10:14:01 UTC (rev 830)
@@ -1,9 +1,20 @@
-mafft (6.240-2) unstable; urgency=low
+mafft (6.240-2) UNRELEASED; urgency=low
 
+  [ Charles Plessy ]
   * Moved the Homepage: field out from the package's description.
 
- -- Charles Plessy <charles-debian-nospam at plessy.org>  Fri, 21 Sep 2007 23:06:14 +0900
+  [ David Paleino ]
+  * debian/mafft.1, debian/mafft-homologs.1 added - manpages built statically.
+  * debian/control:
+    - B-D updated (see above)
+    - added myself to Uploaders
+    - moved XS-Vcs-* fields to Vcs-*
+  * debian/rules:
+    - reflecting static build of manpages
+    - minor changes
 
+ -- David Paleino <d.paleino at gmail.com>  Sun, 18 Nov 2007 11:12:06 +0100
+
 mafft (6.240-1) unstable; urgency=low
 
   * Initial release (Closes: #409640)

Modified: trunk/packages/mafft/trunk/debian/control
===================================================================
--- trunk/packages/mafft/trunk/debian/control	2007-11-18 10:07:41 UTC (rev 829)
+++ trunk/packages/mafft/trunk/debian/control	2007-11-18 10:14:01 UTC (rev 830)
@@ -2,11 +2,12 @@
 Section: science
 Priority: optional
 Maintainer: Debian-Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
-Uploaders: Charles Plessy <charles-debian-nospam at plessy.org>
-Build-Depends: debhelper (>= 5), xsltproc, docbook-xsl, docbook-xml
+Uploaders: Charles Plessy <charles-debian-nospam at plessy.org>,
+ David Paleino <d.paleino at gmail.com>
+Build-Depends: debhelper (>= 5)
 Standards-Version: 3.7.2
-XS-Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/mafft/trunk/
-XS-Vcs-Svn: svn://svn.debian.org/svn/debian-med/trunk/packages/mafft
+Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/mafft/trunk/
+Vcs-Svn: svn://svn.debian.org/svn/debian-med/trunk/packages/mafft/
 Homepage: http://align.bmr.kyushu-u.ac.jp/mafft/software/
 
 Package: mafft

Added: trunk/packages/mafft/trunk/debian/mafft-homologs.1
===================================================================
--- trunk/packages/mafft/trunk/debian/mafft-homologs.1	                        (rev 0)
+++ trunk/packages/mafft/trunk/debian/mafft-homologs.1	2007-11-18 10:14:01 UTC (rev 830)
@@ -0,0 +1,108 @@
+.\"     Title: MAFFT-HOMOLOGS
+.\"    Author: Kazutaka Katoh <katoh_at_bioreg.kyushu-u.ac.jp.>
+.\" Generator: DocBook XSL Stylesheets v1.73.2 <http://docbook.sf.net/>
+.\"      Date: 2007-06-09
+.\"    Manual: Mafft Manual
+.\"    Source: mafft-homologs 2.1
+.\"
+.TH "MAFFT\-HOMOLOGS" "1" "2007\-06\-09" "mafft-homologs 2.1" "Mafft Manual"
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.SH "NAME"
+mafft-homologs - aligns sequences together with homologues automatically collected from SwissProt via NCBI BLAST
+.SH "SYNOPSIS"
+.HP 15
+\fBmafft\-homologs\fR [\fBoptions\fR] \fIinput\fR [>\ \fIoutput\fR]
+.SH "DESCRIPTION"
+.PP
+The accuracy of an alignment of a few distantly related sequences is considerably improved when being aligned together with their close homologs\. The reason for the improvement is probably the same as that for PSI\-BLAST\. That is, the positions of highly conserved residues, those with many gaps and other additional information is brought by close homologs\. According to Katoh et al\. (2005), the improvement by adding close homologs is 10% or so, which is comparable to the improvement by incorporating structural information of a pair of sequences\. Mafft\-homologs in a mafft server works like this:
+.sp
+.RS 4
+\h'-04' 1.\h'+02'Collect a number (50 by default) of close homologs (E=1e\-10 by default) of the input sequences\.
+.RE
+.sp
+.RS 4
+\h'-04' 2.\h'+02'Align the input sequences and homologs all together using the L\-INS\-i strategy\.
+.RE
+.sp
+.RS 4
+\h'-04' 3.\h'+02'Remove the homologs\.
+.RE
+.SH "OPTIONS"
+.PP
+\fB\-a\fR \fI\fIn\fR\fR
+.RS 4
+The number of collected sequences (default: 50)\.
+.RE
+.PP
+\fB\-e\fR \fI\fIn\fR\fR
+.RS 4
+Threshold value (default: 1e\-10)\.
+.RE
+.PP
+\fB\-o\fR \fI\fIxxx\fR\fR
+.RS 4
+options for mafft (default: " \-\-op 1\.53 \-\-ep 0\.123 \-\-maxiterate 1000")\.
+.RE
+.PP
+\fB\-l\fR
+.RS 4
+Locally carries out blast searches instead of NCBI blast (requires locally installed blast and a database)\.
+.RE
+.PP
+\fB\-f\fR
+.RS 4
+Outputs collected homologues also (default: off)\.
+.RE
+.PP
+\fB\-w\fR
+.RS 4
+entire sequences are subjected to BLAST search (default: well\-aligned region only)
+.RE
+.SH "REQUIREMENTS"
+.PP
+Mafft\-homologs requires a version of mafft higher than 5\.58\.
+.SH "REFERENCES"
+.PP
+Katoh, Kuma, Toh and Miyata (Nucleic Acids Res\. 33:511\-518, 2005) MAFFT version 5: improvement in accuracy of multiple sequence alignment\.
+.SH "SEE ALSO"
+.PP
+
+\fBmafft\fR(1)
+.SH "AUTHORS"
+.PP
+\fBKazutaka Katoh\fR <\&katoh_at_bioreg\.kyushu\-u\.ac\.jp\.\&>
+.sp -1n
+.IP "" 4
+Wrote Mafft\.
+.PP
+\fBCharles Plessy\fR <\&charles\-debian\-nospam at plessy\.org\&>
+.sp -1n
+.IP "" 4
+Wrote this manpage in DocBook XML for the Debian distribution, using Mafft\'s homepage as a template\.
+.SH "COPYRIGHT"
+Copyright \(co 2002-2007 Kazutaka Katoh (mafft)
+.br
+Copyright \(co 2007 Charles Plessy (this manpage)
+.br
+.PP
+Mafft and its manpage are offered under the following conditions:
+.PP
+Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met:
+.sp
+.RS 4
+\h'-04' 1.\h'+02'Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer\.
+.RE
+.sp
+.RS 4
+\h'-04' 2.\h'+02'Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution\.
+.RE
+.sp
+.RS 4
+\h'-04' 3.\h'+02'The name of the author may not be used to endorse or promote products derived from this software without specific prior written permission\.
+.RE
+.PP
+THIS SOFTWARE IS PROVIDED BY THE AUTHOR "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED\. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE\.
+.sp

Added: trunk/packages/mafft/trunk/debian/mafft.1
===================================================================
--- trunk/packages/mafft/trunk/debian/mafft.1	                        (rev 0)
+++ trunk/packages/mafft/trunk/debian/mafft.1	2007-11-18 10:14:01 UTC (rev 830)
@@ -0,0 +1,366 @@
+.\"     Title: MAFFT
+.\"    Author: Kazutaka Katoh <katoh_at_bioreg.kyushu-u.ac.jp.>
+.\" Generator: DocBook XSL Stylesheets v1.73.2 <http://docbook.sf.net/>
+.\"      Date: 2007-06-09
+.\"    Manual: Mafft Manual
+.\"    Source: mafft 6.240
+.\"
+.TH "MAFFT" "1" "2007\-06\-09" "mafft 6.240" "Mafft Manual"
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.SH "NAME"
+mafft - Multiple alignment program for amino acid or nucleotide sequences
+.SH "SYNOPSIS"
+.HP 6
+\fBmafft\fR [\fBoptions\fR] \fIinput\fR [>\ \fIoutput\fR]
+.HP 6
+\fBlinsi\fR \fIinput\fR [>\ \fIoutput\fR]
+.HP 6
+\fBginsi\fR \fIinput\fR [>\ \fIoutput\fR]
+.HP 6
+\fBeinsi\fR \fIinput\fR [>\ \fIoutput\fR]
+.HP 7
+\fBfftnsi\fR \fIinput\fR [>\ \fIoutput\fR]
+.HP 6
+\fBfftns\fR \fIinput\fR [>\ \fIoutput\fR]
+.HP 14
+\fBmafft\-profile\fR \fIgroup1\fR \fIgroup2\fR [>\ \fIoutput\fR]
+.SH "DESCRIPTION"
+.PP
+\fBMAFFT\fR
+is a multiple sequence alignment program for unix\-like operating systems\. It offers a range of multiple alignment methods\.
+.SS "Accuracy\-oriented methods:"
+.sp
+.RS 4
+\h'-04'\(bu\h'+03'L\-INS\-i (probably most accurate; recommended for <200 sequences; iterative refinement method incorporating local pairwise alignment information):
+.HP 6
+\fBmafft\fR \fB\-\-localpair\fR \fB\-\-maxiterate\fR\ \fI1000\fR \fIinput\fR [>\ \fIoutput\fR]
+.HP 6
+\fBlinsi\fR \fIinput\fR [>\ \fIoutput\fR]
+.RE
+.sp
+.RS 4
+\h'-04'\(bu\h'+03'G\-INS\-i (suitable for sequences of similar lengths; recommended for <200 sequences; iterative refinement method incorporating global pairwise alignment information):
+.HP 6
+\fBmafft\fR \fB\-\-globalpair\fR \fB\-\-maxiterate\fR\ \fI1000\fR \fIinput\fR [>\ \fIoutput\fR]
+.HP 6
+\fBginsi\fR \fIinput\fR [>\ \fIoutput\fR]
+.RE
+.sp
+.RS 4
+\h'-04'\(bu\h'+03'E\-INS\-i (suitable for sequences containing large unalignable regions; recommended for <200 sequences):
+.HP 6
+\fBmafft\fR \fB\-\-ep\fR\ \fI0\fR \fB\-\-genafpair\fR \fB\-\-maxiterate\fR\ \fI1000\fR \fIinput\fR [>\ \fIoutput\fR]
+.HP 6
+\fBeinsi\fR \fIinput\fR [>\ \fIoutput\fR]
+.br
+
+For E\-INS\-i, the
+\fB\-\-ep\fR
+\fI0\fR
+option is recommended to allow large gaps\.
+.RE
+.SS "Speed\-oriented methods:"
+.sp
+.RS 4
+\h'-04'\(bu\h'+03'FFT\-NS\-i (iterative refinement method; two cycles only):
+.HP 6
+\fBmafft\fR \fB\-\-retree\fR\ \fI2\fR \fB\-\-maxiterate\fR\ \fI2\fR \fIinput\fR [>\ \fIoutput\fR]
+.HP 7
+\fBfftnsi\fR \fIinput\fR [>\ \fIoutput\fR]
+.RE
+.sp
+.RS 4
+\h'-04'\(bu\h'+03'FFT\-NS\-i (iterative refinement method; max\. 1000 iterations):
+.HP 6
+\fBmafft\fR \fB\-\-retree\fR\ \fI2\fR \fB\-\-maxiterate\fR\ \fI1000\fR \fIinput\fR [>\ \fIoutput\fR]
+.RE
+.sp
+.RS 4
+\h'-04'\(bu\h'+03'FFT\-NS\-2 (fast; progressive method):
+.HP 6
+\fBmafft\fR \fB\-\-retree\fR\ \fI2\fR \fB\-\-maxiterate\fR\ \fI0\fR \fIinput\fR [>\ \fIoutput\fR]
+.HP 6
+\fBfftns\fR \fIinput\fR [>\ \fIoutput\fR]
+.RE
+.sp
+.RS 4
+\h'-04'\(bu\h'+03'FFT\-NS\-1 (very fast; recommended for >2000 sequences; progressive method with a rough guide tree):
+.HP 6
+\fBmafft\fR \fB\-\-retree\fR\ \fI1\fR \fB\-\-maxiterate\fR\ \fI0\fR \fIinput\fR [>\ \fIoutput\fR]
+.RE
+.sp
+.RS 4
+\h'-04'\(bu\h'+03'NW\-NS\-PartTree\-1 (recommended for ?50,000 sequences; progressive method with the PartTree algorithm):
+.HP 6
+\fBmafft\fR \fB\-\-retree\fR\ \fI1\fR \fB\-\-maxiterate\fR\ \fI0\fR \fB\-\-parttree\fR \fIinput\fR [>\ \fIoutput\fR]
+.RE
+.SS "Group\-to\-group alignments"
+.HP 14
+\fBmafft\-profile\fR \fIgroup1\fR \fIgroup2\fR [>\ \fIoutput\fR]
+.PP
+or:
+.HP 6
+\fBmafft\fR \fB\-\-maxiterate\fR\ \fI1000\fR \fB\-\-seed\fR\ \fIgroup1\fR \fB\-\-seed\fR\ \fIgroup2\fR /dev/null [>\ \fIoutput\fR]
+.SH "OPTIONS"
+.PP
+\fB\-\-auto\fR
+.RS 4
+.RE
+.PP
+\fB\-\-clustalout\fR
+.RS 4
+.RE
+.PP
+\fB\-\-reorder\fR
+.RS 4
+.RE
+.PP
+\fB\-\-inputorder\fR
+.RS 4
+.RE
+.PP
+\fB\-\-algq\fR
+.RS 4
+.RE
+.PP
+\fB\-\-groupsize\fR
+.RS 4
+.RE
+.PP
+\fB\-\-partsize\fR
+.RS 4
+.RE
+.PP
+\fB\-\-parttree\fR
+.RS 4
+.RE
+.PP
+\fB\-\-dpparttree\fR
+.RS 4
+.RE
+.PP
+\fB\-\-fastaparttree\fR
+.RS 4
+.RE
+.PP
+\fB\-\-treeout\fR
+.RS 4
+.RE
+.PP
+\fB\-\-fastswpair\fR
+.RS 4
+.RE
+.PP
+\fB\-\-fastapair\fR
+.RS 4
+.RE
+.PP
+\fB\-\-noscore\fR
+.RS 4
+.RE
+.PP
+\fB\-\-6merpair\fR
+.RS 4
+.RE
+.PP
+\fB\-\-blastpair\fR
+.RS 4
+.RE
+.PP
+\fB\-\-globalpair\fR
+.RS 4
+.RE
+.PP
+\fB\-\-localpair\fR
+.RS 4
+.RE
+.PP
+\fB\-\-genafpair\fR
+.RS 4
+.RE
+.PP
+\fB\-\-memsave\fR
+.RS 4
+.RE
+.PP
+\fB\-\-nuc\fR
+.RS 4
+.RE
+.PP
+\fB\-\-amino\fR
+.RS 4
+.RE
+.PP
+\fB\-\-fft\fR
+.RS 4
+.RE
+.PP
+\fB\-\-nofft\fR
+.RS 4
+.RE
+.PP
+\fB\-\-quiet\fR
+.RS 4
+.RE
+.PP
+\fB\-\-coreext\fR
+.RS 4
+.RE
+.PP
+\fB\-\-core\fR
+.RS 4
+.RE
+.PP
+\fB\-\-maxiterate\fR
+.RS 4
+.RE
+.PP
+\fB\-\-retree\fR
+.RS 4
+.RE
+.PP
+\fB\-\-aamatrix\fR
+.RS 4
+.RE
+.PP
+\fB\-\-fmodel\fR
+.RS 4
+.RE
+.PP
+\fB\-\-jtt\fR
+.RS 4
+.RE
+.PP
+\fB\-\-tm\fR
+.RS 4
+.RE
+.PP
+\fB\-\-bl\fR
+.RS 4
+.RE
+.PP
+\fB\-\-weighti\fR
+.RS 4
+.RE
+.PP
+\fB\-\-op\fR
+.RS 4
+.RE
+.PP
+\fB\-\-ep\fR
+.RS 4
+.RE
+.PP
+\fB\-\-lop\fR
+.RS 4
+.RE
+.PP
+\fB\-\-LOP\fR
+.RS 4
+.RE
+.PP
+\fB\-\-lep\fR
+.RS 4
+.RE
+.PP
+\fB\-\-lexp\fR
+.RS 4
+.RE
+.PP
+\fB\-\-LEXP\fR
+.RS 4
+.RE
+.PP
+\fB\-\-corethr\fR
+.RS 4
+.RE
+.PP
+\fB\-\-corewin\fR
+.RS 4
+.RE
+.PP
+\fB\-\-seed\fR
+.RS 4
+.RE
+.SH "FILES"
+.PP
+Mafft stores the input sequences and other files in a temporary directory, which by default is located in
+\fI/tmp\fR\.
+.SH "ENVIONMENT"
+.PP
+\fBMAFFT_BINARIES\fR
+.RS 4
+Indicates the location of the binary files used by mafft\. By default, they are searched in
+\fI/usr/local/lib/mafft\fR, but on Debian systems, they are searched in
+\fI/usr/lib/mafft\fR\.
+.RE
+.PP
+\fBFASTA_4_MAFFT\fR
+.RS 4
+This variable can be set to indicate to mafft the location to the fasta34 program if it is not in the PATH\.
+.RE
+.SH "SEE ALSO"
+.PP
+
+\fBmafft-homologs\fR(1)
+.SH "REFERENCES"
+.SS "In English"
+.sp
+.RS 4
+\h'-04'\(bu\h'+03'Katoh and Toh (Bioinformatics 23:372\-374, 2007) PartTree: an algorithm to build an approximate tree from a large number of unaligned sequences (describes the PartTree algorithm)\.
+.RE
+.sp
+.RS 4
+\h'-04'\(bu\h'+03'Katoh, Kuma, Toh and Miyata (Nucleic Acids Res\. 33:511\-518, 2005) MAFFT version 5: improvement in accuracy of multiple sequence alignment (describes [ancestral versions of] the G\-INS\-i, L\-INS\-i and E\-INS\-i strategies)
+.RE
+.sp
+.RS 4
+\h'-04'\(bu\h'+03'Katoh, Misawa, Kuma and Miyata (Nucleic Acids Res\. 30:3059\-3066, 2002) MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform (describes the FFT\-NS\-1, FFT\-NS\-2 and FFT\-NS\-i strategies)
+.RE
+.SS "In Japanese"
+.sp
+.RS 4
+\h'-04'\(bu\h'+03'Katoh and Misawa (???? 46:312\-317, 2006) Multiple Sequence Alignments: the Next Generation
+.RE
+.sp
+.RS 4
+\h'-04'\(bu\h'+03'Katoh and Kuma (????? 44:102\-108, 2006) Jissen\-teki Multiple Alignment
+.RE
+.SH "AUTHORS"
+.PP
+\fBKazutaka Katoh\fR <\&katoh_at_bioreg\.kyushu\-u\.ac\.jp\.\&>
+.sp -1n
+.IP "" 4
+Wrote Mafft\.
+.PP
+\fBCharles Plessy\fR <\&charles\-debian\-nospam at plessy\.org\&>
+.sp -1n
+.IP "" 4
+Wrote this manpage in DocBook XML for the Debian distribution, using Mafft\'s homepage as a template\.
+.SH "COPYRIGHT"
+Copyright \(co 2002-2007 Kazutaka Katoh (mafft)
+.br
+Copyright \(co 2007 Charles Plessy (this manpage)
+.br
+.PP
+Mafft and its manpage are offered under the following conditions:
+.PP
+Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met:
+.sp
+.RS 4
+\h'-04' 1.\h'+02'Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer\.
+.RE
+.sp
+.RS 4
+\h'-04' 2.\h'+02'Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution\.
+.RE
+.sp
+.RS 4
+\h'-04' 3.\h'+02'The name of the author may not be used to endorse or promote products derived from this software without specific prior written permission\.
+.RE
+.PP
+THIS SOFTWARE IS PROVIDED BY THE AUTHOR "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED\. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE\.
+.sp

Modified: trunk/packages/mafft/trunk/debian/rules
===================================================================
--- trunk/packages/mafft/trunk/debian/rules	2007-11-18 10:07:41 UTC (rev 829)
+++ trunk/packages/mafft/trunk/debian/rules	2007-11-18 10:14:01 UTC (rev 830)
@@ -9,7 +9,8 @@
       -''-nonet \
       -''-param man.charmap.use.subset "0" \
       -''-param make.year.ranges "1" \
-      -''-param make.single.year.ranges "1"
+      -''-param make.single.year.ranges "1" \
+      -o debian/
 
 
 CFLAGS = -Wall -g
@@ -26,11 +27,11 @@
 mafft-homologs.1: debian/mafft-homologs.1.xml
 	$(XP) $<
 
-build-stamp: build
-build: mafft.1 mafft-homologs.1
+build: build-stamp
+build-stamp:
 	dh_testdir
 	$(MAKE) -C src PREFIX=/usr/lib/mafft
-	touch build-stamp
+	touch $@
 
 MAFFT = MAFFT_BINARIES=$(CURDIR)/binaries scripts/mafft
 
@@ -46,7 +47,7 @@
 	dh_testdir
 	dh_testroot
 	[ ! -f Makefile ] || $(MAKE) -C src clean
-	dh_clean mafft.1 mafft-homologs.1 build-stamp
+	dh_clean build-stamp
 
 install: build-stamp test
 	dh_testdir
@@ -57,14 +58,13 @@
 	mv debian/mafft/usr/bin/mafft-homologs.rb debian/mafft/usr/bin/mafft-homologs
 
 binary-indep: build install
-
 binary-arch: build install
 	dh_testdir
 	dh_testroot
 	dh_installchangelogs 
 	dh_installdocs
 	dh_install test usr/share/doc/mafft/
-	dh_installman mafft.1 mafft-homologs.1
+	dh_installman debian/mafft.1 debian/mafft-homologs.1
 	dh_link
 	dh_strip
 	dh_compress

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