[med-svn] r200 - in trunk/packages/mafft/trunk: . debian
Charles Plessy
charles-guest at alioth.debian.org
Thu Feb 8 02:25:09 CET 2007
Author: charles-guest
Date: 2007-02-08 02:25:08 +0100 (Thu, 08 Feb 2007)
New Revision: 200
Added:
trunk/packages/mafft/trunk/debian/
trunk/packages/mafft/trunk/debian/README.Debian
trunk/packages/mafft/trunk/debian/changelog
trunk/packages/mafft/trunk/debian/compat
trunk/packages/mafft/trunk/debian/control
trunk/packages/mafft/trunk/debian/copyright
trunk/packages/mafft/trunk/debian/dirs
trunk/packages/mafft/trunk/debian/rules
trunk/packages/mafft/trunk/debian/watch
Log:
Load newtrunk into trunk/packages/mafft/trunk.
Added: trunk/packages/mafft/trunk/debian/README.Debian
===================================================================
--- trunk/packages/mafft/trunk/debian/README.Debian 2007-02-08 01:24:14 UTC (rev 199)
+++ trunk/packages/mafft/trunk/debian/README.Debian 2007-02-08 01:25:08 UTC (rev 200)
@@ -0,0 +1,21 @@
+mafft for Debian
+----------------
+
+Some test are available:
+
+% cd /usr/share/doc/mafft/test
+% mafft sample > test.fftns2 # FFT-NS-2
+% mafft --maxiterate 100 sample > test.fftnsi # FFT-NS-i
+% mafft --globalpair sample > test.gins1 # G-INS-1
+% mafft --globalpair --maxiterate 100 sample > test.ginsi # G-INS-i
+% mafft --localpair sample > test.lins1 # L-INS-1
+% mafft --localpair --maxiterate 100 sample > test.linsi # L-INS-i
+% diff test.fftns2 sample.fftns2
+% diff test.fftnsi sample.fftnsi
+% diff test.gins1 sample.gins1
+% diff test.ginsi sample.ginsi
+% diff test.lins1 sample.lins1
+% diff test.linsi sample.linsi
+
+
+ -- Charles Plessy <charles-debian-nospam at plessy.org> Wed, 7 Feb 2007 21:44:40 +0900
Added: trunk/packages/mafft/trunk/debian/changelog
===================================================================
--- trunk/packages/mafft/trunk/debian/changelog 2007-02-08 01:24:14 UTC (rev 199)
+++ trunk/packages/mafft/trunk/debian/changelog 2007-02-08 01:25:08 UTC (rev 200)
@@ -0,0 +1,6 @@
+mafft (6.236~beta-1) unstable; urgency=low
+
+ * Initial release (Closes: #409640)
+
+ -- Charles Plessy <charles-debian-nospam at plessy.org> Wed, 7 Feb 2007 21:44:40 +0900
+
Added: trunk/packages/mafft/trunk/debian/compat
===================================================================
--- trunk/packages/mafft/trunk/debian/compat 2007-02-08 01:24:14 UTC (rev 199)
+++ trunk/packages/mafft/trunk/debian/compat 2007-02-08 01:25:08 UTC (rev 200)
@@ -0,0 +1 @@
+5
Added: trunk/packages/mafft/trunk/debian/control
===================================================================
--- trunk/packages/mafft/trunk/debian/control 2007-02-08 01:24:14 UTC (rev 199)
+++ trunk/packages/mafft/trunk/debian/control 2007-02-08 01:25:08 UTC (rev 200)
@@ -0,0 +1,32 @@
+Source: mafft
+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
+Standards-Version: 3.7.2
+
+Package: mafft
+Architecture: any
+Depends: ${shlibs:Depends}, ${misc:Depends}
+Description: Multiple alignment program for amino acid or nucleotide sequences
+ MAFFT is a multiple sequence alignment program, which offers three
+ accuracy-oriented methods:
+ * L-INS-i (probably most accurate; recommended for <200 sequences;
+ iterative refinement method incorporating local pairwise alignment
+ information),
+ * G-INS-i (suitable for sequences of similar lengths; recommended for
+ <200 sequences; iterative refinement method incorporating global
+ pairwise alignment information),
+ * E-INS-i (suitable for sequences containing large unalignable regions;
+ recommended for <200 sequences),
+ and five speed-oriented methods:
+ * FFT-NS-i (iterative refinement method; two cycles only),
+ * FFT-NS-i (iterative refinement method; max. 1000 iterations),
+ * FFT-NS-2 (fast; progressive method),
+ * FFT-NS-1 (very fast; recommended for >2000 sequences; progressive
+ method with a rough guide tree),
+ * NW-NS-PartTree-1 (recommended for ∼50,000 sequences; progressive
+ method with the PartTree algorithm).
+ .
+ Homepage: http://align.bmr.kyushu-u.ac.jp/mafft/software/
Added: trunk/packages/mafft/trunk/debian/copyright
===================================================================
--- trunk/packages/mafft/trunk/debian/copyright 2007-02-08 01:24:14 UTC (rev 199)
+++ trunk/packages/mafft/trunk/debian/copyright 2007-02-08 01:25:08 UTC (rev 200)
@@ -0,0 +1,35 @@
+This package was debianized by Charles Plessy <charles-debian-nospam at plessy.org> on
+Wed, 7 Feb 2007 21:44:40 +0900.
+
+It was downloaded from http://align.bmr.kyushu-u.ac.jp/mafft/software/mafft-6.236-src.tgz
+
+Upstream Author: Kazutaka Katoh <katoh at bioreg.kyushu-u.ac.jp>
+
+Copyright: 2006 Kazutaka Katoh
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are met:
+
+Redistributions of source code must retain the above copyright notice, this
+list of conditions and the following disclaimer. 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.
+
+The name of the author may not be used to endorse or promote products derived
+from this software without specific prior written permission.
+
+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.
+
+--
+The Debian packaging is (C) 2007, Charles Plessy <charles-debian-nospam at plessy.org> and
+is licensed under the same licence as mafft itself.
Added: trunk/packages/mafft/trunk/debian/dirs
===================================================================
--- trunk/packages/mafft/trunk/debian/dirs 2007-02-08 01:24:14 UTC (rev 199)
+++ trunk/packages/mafft/trunk/debian/dirs 2007-02-08 01:25:08 UTC (rev 200)
@@ -0,0 +1,2 @@
+usr/lib/mafft
+usr/share/doc/mafft/test/
Added: trunk/packages/mafft/trunk/debian/rules
===================================================================
--- trunk/packages/mafft/trunk/debian/rules 2007-02-08 01:24:14 UTC (rev 199)
+++ trunk/packages/mafft/trunk/debian/rules 2007-02-08 01:25:08 UTC (rev 200)
@@ -0,0 +1,57 @@
+#!/usr/bin/make -f
+# -*- makefile -*-
+# Build rules for the Debian package mafft.
+
+# Uncomment this to turn on verbose mode.
+#export DH_VERBOSE=1
+
+CFLAGS = -Wall -g
+
+ifneq (,$(findstring noopt,$(DEB_BUILD_OPTIONS)))
+ CFLAGS += -O0
+else
+ CFLAGS += -O2
+endif
+
+build:
+ dh_testdir
+ # Add here commands to compile the package.
+ $(MAKE) -C src
+ #docbook-to-man debian/mafft.sgml > mafft.1
+
+test:
+
+clean:
+ dh_testdir
+ dh_testroot
+ -$(MAKE) -C src clean
+ dh_clean
+
+install: build test
+ dh_testdir
+ dh_testroot
+ dh_clean -k
+ dh_installdirs
+ $(MAKE) -C src PREFIX=$(CURDIR)/debian/mafft/usr/lib/mafft install
+
+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
+ 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/mafft/trunk/debian/rules
___________________________________________________________________
Name: svn:executable
+ *
Added: trunk/packages/mafft/trunk/debian/watch
===================================================================
--- trunk/packages/mafft/trunk/debian/watch 2007-02-08 01:24:14 UTC (rev 199)
+++ trunk/packages/mafft/trunk/debian/watch 2007-02-08 01:25:08 UTC (rev 200)
@@ -0,0 +1,22 @@
+# Example watch control file for uscan
+# Rename this file to "watch" and then you can run the "uscan" command
+# to check for upstream updates and more.
+# See uscan(1) for format
+
+# Compulsory line, this is a version 3 file
+version=3
+
+# Uncomment to examine a Webpage
+# <Webpage URL> <string match>
+#http://www.example.com/downloads.php mafft-(.*)\.tar\.gz
+
+# Uncomment to examine a Webserver directory
+#http://www.example.com/pub/mafft-(.*)\.tar\.gz
+
+# Uncommment to examine a FTP server
+#ftp://ftp.example.com/pub/mafft-(.*)\.tar\.gz debian uupdate
+
+# Uncomment to find new files on sourceforge, for debscripts >= 2.9
+# http://sf.net/mafft/mafft-(.*)\.tar\.gz
+
+
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