[med-svn] r1146 - in trunk/packages/clustalw/trunk: . debian
charles-guest at alioth.debian.org
charles-guest at alioth.debian.org
Wed Jan 16 13:22:51 UTC 2008
Author: charles-guest
Date: 2008-01-16 13:22:51 +0000 (Wed, 16 Jan 2008)
New Revision: 1146
Added:
trunk/packages/clustalw/trunk/README
trunk/packages/clustalw/trunk/debian/patches/
Removed:
trunk/packages/clustalw/trunk/LICENCE
trunk/packages/clustalw/trunk/debian/patches/
trunk/packages/clustalw/trunk/debian/shlibs.local
Modified:
trunk/packages/clustalw/trunk/debian/changelog
trunk/packages/clustalw/trunk/debian/clustalw.docs
trunk/packages/clustalw/trunk/debian/clustalw.install
trunk/packages/clustalw/trunk/debian/clustalx.docs
trunk/packages/clustalw/trunk/debian/clustalx.install
trunk/packages/clustalw/trunk/debian/control
trunk/packages/clustalw/trunk/debian/copyright
trunk/packages/clustalw/trunk/debian/rules
trunk/packages/clustalw/trunk/debian/watch
Log:
new upstream release, the packaging is still buggy and clustalw is not built
Deleted: trunk/packages/clustalw/trunk/LICENCE
===================================================================
--- trunk/packages/clustalw/trunk/LICENCE 2008-01-15 20:04:31 UTC (rev 1145)
+++ trunk/packages/clustalw/trunk/LICENCE 2008-01-16 13:22:51 UTC (rev 1146)
@@ -1,29 +0,0 @@
-**********************
-LICENCE FOR CLUSTAL W
-**********************
-
-Clustal W (hereafter "the program") is copyright (c) 1994-1998 by Julie D.
-Thompson, Desmond G. Higgins and Toby J. Gibson.
-
-Permission is granted to copy, distribute and use the program provided no fee
-is charged for it and provided that this copyright and licence notice is not
-removed or altered.
-
-The full source code of the program is provided free. You should not
-distribute a modified version of the program without obtaining the permission
-of the authors. You must keep the original copyright and licence notice. You
-must also document clearly the modifications you have made. You must make
-clear that this is not the original version.
-
-Commercial distributors of Clustal W are requested to contact the Clustal W
-authors in order to take out a non-exclusive licence. See the README file
-included with Clustal W for a rationale.
-
-You should understand that this software is provided as-is. The authors make
-no claims towards its suitability for any purpose and accept absolutely no
-liability for any damages the program may cause. Use at your own risk.
-
-
-
-
-
Added: trunk/packages/clustalw/trunk/README
===================================================================
--- trunk/packages/clustalw/trunk/README (rev 0)
+++ trunk/packages/clustalw/trunk/README 2008-01-16 13:22:51 UTC (rev 1146)
@@ -0,0 +1,72 @@
+CLUSTAL W and CLUSTAL X Multiple Sequence Alignment Programs
+ (version 2.0, 26 November 2007)
+
+Contact email address: clustalw at ucd.ie
+
+For details and citation purposes see paper "Clustal W and Clustal X version 2.0", Larkin M., et al. Bioinformatics 2007 23(21):2947-2948
+http://bioinformatics.oxfordjournals.org/cgi/content/full/23/21/2947
+
+Clustal X provides a window-based user interface to the ClustalW multiple
+alignment program.
+
+This directory contains the files:
+
+clustalw-linux-i386-2.0.tar.gz - a compressed tar file with a linux binary for ClustalW (Debian/Ubuntu)
+
+clustalw-linux-src-2.0.tar.gz - a compressed tar file with source code for Clustalw for linux
+
+clustalw-mac-universal-2.0.tgz - a compressed tar file with a Mac universal binary
+
+clustalw-windows-xp-2.0.zip - a compressed Windows XP archive
+
+clustalw-windows-xp-src.tar.gz - a compressed tar file containing the source code for ClustalW for windows
+
+clustalx-linux-i386-2.0.tar.gz - a compressed tar file with the linux binary for ClustalX (Debian/Ubuntu)
+
+clustalx-linux-rhel3-libcppstatic-i386-2.0.tgz - a compressed tar file with the linux binary for ClustalX (Red Hat Enterprise edition 3 using the XFree X-windows libraries)
+
+clustalx-mac-universal-2.0.dmg - a disk image for the Mac universal binary for ClustalX
+
+clustalx-windows-xp-2.0.zip - a compressed Windows XP archive with the PC binary for ClustalX
+
+clustalx-src-2.0.zip - a compressed tar file with the source code for ClustalX (All platforms - requires Qt GUI framework from Trolltech to compile)
+
+
+Supported systems
+----------------------------------------------------------
+Windows XP
+
+Mac OSX 10.3.9 or higher
+
+Linux (debian and red hat binaries)
+
+We have successfully run the binaries on:
+Ubuntu 6.10 Edge Eft
+Red Hat Enterprise Edition 3.0
+Debian 4.0 testing
+
+
+Contributed binaries
+----------------------------------------------------------
+For operating systems that we cannot support ourselves we
+try to maintain a collection of binaries that have been
+compiled by other users. These can be found in the sub-directory "contributed"
+
+Acknowledgements
+----------------------------------------------------------
+Science Foundation Ireland who provided the funding which enabled the development of Clustal2.0
+
+Bug Tracking
+----------------------------------------------------------
+We track bugs in Clustal in a publicly viewable bugzilla instance. You can find it at: http://bioinformatics.ucd.ie/bugzilla
+If users find a bug or have issues running clustal2.0 they should contact the development team at clustalw at ucd.ie
+
+Known issues
+----------------------------------------------------------
+1. ClustalX2.0 doesn't run on Mac OSX 10.3.8 or lower
+Resolution: upgrade Mac OS to OSX 10.3.9 or better
+
+
+Next Release
+----------------------------------------------------------
+The next release 2.0.1 is scheduled for 29th January 2008
Modified: trunk/packages/clustalw/trunk/debian/changelog
===================================================================
--- trunk/packages/clustalw/trunk/debian/changelog 2008-01-15 20:04:31 UTC (rev 1145)
+++ trunk/packages/clustalw/trunk/debian/changelog 2008-01-16 13:22:51 UTC (rev 1146)
@@ -1,5 +1,10 @@
-clustalw (1.83-4) UNRELEASED; urgency=low
+clustalw (2.0-1) UNRELEASED; urgency=low
+ * New upstream release:
+ - Uses Qt instead of lesstif.
+ - Includes new code for UPGMA guide trees.
+ - Includes iterative alignment facility.
+ * debian/copyright made machine-readable.
* Association between Clustal X and .aln files:
- text/x-clustalw-alignment associated to clustalx in clustalx.desktop.
- .aln declared as text/x-clustalw-alignment in clustalx.sharedmimeinfo.
Modified: trunk/packages/clustalw/trunk/debian/clustalw.docs
===================================================================
--- trunk/packages/clustalw/trunk/debian/clustalw.docs 2008-01-15 20:04:31 UTC (rev 1145)
+++ trunk/packages/clustalw/trunk/debian/clustalw.docs 2008-01-16 13:22:51 UTC (rev 1146)
@@ -1,4 +1 @@
-README_W
-clustalv.doc
-clustalw.doc
-clustalw.ms
+README
Modified: trunk/packages/clustalw/trunk/debian/clustalw.install
===================================================================
--- trunk/packages/clustalw/trunk/debian/clustalw.install 2008-01-15 20:04:31 UTC (rev 1145)
+++ trunk/packages/clustalw/trunk/debian/clustalw.install 2008-01-16 13:22:51 UTC (rev 1146)
@@ -1,2 +1,2 @@
-clustalw usr/bin
-clustalw_help usr/share/clustalw
+#clustalw2.1/clustalw usr/bin
+clustalw2.1/clustalw_help usr/share/clustalw
Modified: trunk/packages/clustalw/trunk/debian/clustalx.docs
===================================================================
--- trunk/packages/clustalw/trunk/debian/clustalx.docs 2008-01-15 20:04:31 UTC (rev 1145)
+++ trunk/packages/clustalw/trunk/debian/clustalx.docs 2008-01-16 13:22:51 UTC (rev 1146)
@@ -1,3 +1 @@
-README_X
-clustalx.html
-
+README
Modified: trunk/packages/clustalw/trunk/debian/clustalx.install
===================================================================
--- trunk/packages/clustalw/trunk/debian/clustalx.install 2008-01-15 20:04:31 UTC (rev 1145)
+++ trunk/packages/clustalw/trunk/debian/clustalx.install 2008-01-16 13:22:51 UTC (rev 1146)
@@ -1,4 +1,3 @@
clustalx usr/bin
-clustalx_help usr/share/clustalw
+clustalx.hlp usr/share/clustalw
debian/clustalx.desktop usr/share/applications
-
Modified: trunk/packages/clustalw/trunk/debian/control
===================================================================
--- trunk/packages/clustalw/trunk/debian/control 2008-01-15 20:04:31 UTC (rev 1145)
+++ trunk/packages/clustalw/trunk/debian/control 2008-01-16 13:22:51 UTC (rev 1146)
@@ -4,42 +4,44 @@
Maintainer: Debian-Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
XS-DM-Upload-Allowed: Yes
Uploaders: Steffen Moeller <moeller at debian.org>, Charles Plessy <charles-debian-nospam at plessy.org>
-Build-Depends: debhelper (>= 5), libncbi6-dev, libvibrant6-dev, lesstif2-dev, quilt
-Standards-Version: 3.7.2
+Build-Depends: debhelper (>= 5), libqt4-dev, quilt
+Standards-Version: 3.7.3
Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/clustalw/trunk/
Vcs-Svn: svn://svn.debian.org/svn/debian-med/trunk/packages/clustalw
XS-Autobuild: yes
+Homepage: http://www.ebi.ac.uk/Tools/clustalw2/
Package: clustalw
Architecture: any
Depends: ${shlibs:Depends}
Suggests: clustalx, seaview
+Enhances: t-coffee
Description: Global multiple nucleotide or peptide sequence alignment
This program performs an alignment of multiple nucleotide or amino
acid sequences. It recognizes the format of input sequences and whether
the sequences are nucleic acid (DNA/RNA) or amino acid (proteins). The
output format may be selected from in various formats for multiple alignments
- such as Phylip or FASTA. ClustalW is very well accepted. An alternative,
+ such as Phylip or FASTA. Clustal W is very well accepted. An alternative,
particularly for fragmented sequences, may be
T-Coffee (http://www.ch.embnet.org/software/TCoffee.html)
DIALIGN (http://dialign.gobics.de/)
or one of the other many algorithms as summarised on
http://www.techfak.uni-bielefeld.de/bcd/Curric/MulAli/welcome.html.
.
- The output of ClustalW can be edited manually but preferably with an alignment
- editor like seaview or within its companion ClustalX.
+ The output of Clustal W can be edited manually but preferably with an alignment
+ editor like SeaView or within its companion Clustal X.
When building a model from your alignment, this can be applied for improved
database searches. The debian package hmmer creates such in form of an HMM.
.
- URL: ftp://ftp-igbmc.u-strasbg.fr/pub/ClustalW/
- URL: ftp://ftp.ebi.ac.uk/pub/software/unix/clustalw/
+ For details and citation purposes see paper "Clustal W and Clustal X version
+ 2.0", Larkin M., et al. Bioinformatics 2007 23(21):2947-2948
Package: clustalx
Architecture: any
-Depends: ${shlibs:Depends}, clustalw
-Suggests: texshade|texlive-latex-extra, boxshade
+Depends: ${shlibs:Depends}
+Suggests: clustalw, texshade|texlive-latex-extra, boxshade
Description: GUI for clustalw
- This package offers a GUI interface for the ClustalW multiple sequence
+ This package offers a GUI interface for the Clustal W multiple sequence
alignment program. It provides an integrated environment for performing
multiple sequence- and profile-alignments to analyse the results.
The sequence alignment is displayed in a window on the screen.
@@ -56,5 +58,5 @@
An alignment quality analysis can be performed and low-scoring segments or
exceptional residues can be highlighted.
.
- URL: ftp://ftp-igbmc.u-strasbg.fr/pub/ClustalX/
- URL: ftp://ftp.ebi.ac.uk/pub/software/unix/clustalx/
+ For details and citation purposes see paper "Clustal W and Clustal X version
+ 2.0", Larkin M., et al. Bioinformatics 2007 23(21):2947-2948
Modified: trunk/packages/clustalw/trunk/debian/copyright
===================================================================
--- trunk/packages/clustalw/trunk/debian/copyright 2008-01-15 20:04:31 UTC (rev 1145)
+++ trunk/packages/clustalw/trunk/debian/copyright 2008-01-16 13:22:51 UTC (rev 1146)
@@ -1,76 +1,75 @@
-This package was debianized by Andreas Tille <tille at debian.org> on
-Sat, 27 Oct 2001 22:16:53 +0200
+X-Format-Specification: http://wiki.debian.org/Proposals/CopyrightFormat
+X-Debianized-By: Stephane Bortzmeyer <bortzmeyer at debian.org>
+X-Debianized-Date: Fri, 28 Aug 1998 16:09:48 +0200
+X-Source-Downloaded-From: ftp://ftp.ebi.ac.uk/pub/software/clustalw2
+X-Upstream-Author: Des Higgins, Julie Thompson and Toby Gibson
-It was downloaded from:
+Files: debian/*
+Copyright: © 1998-1999 Stephane Bortzmeyer <bortzmeyer at debian.org>
+ © 2001 Dr. Guenter Bechly <gbechly at debian.org>
+ © 2001 Adrian Bunk <bunk at fs.tum.de>
+ © 2001-2002 Andreas Tille <tille at debian.org>
+ © 2003-2007 Steffen Möller <moeller at debian.org>
+ © 2006 Kai Hendry <hendry at iki.fi>
+ © 2007 Nelson A. de Oliveira <naoliv at debian.org>
+ © 2007-2008 Charles Plessy <charles-debian-nospam at plessy.org>
+Licence: Unclear
+ The licence of the earlier works was never stated. Some works have been
+ obsoleted by release of version 2.0 — the lesstif migration for instance —
+ but authors are left in the list of copyright holders by courtesy. The work
+ of Charles Plessy can be treated as if it were public domain.
- ftp://ftp-igbmc.u-strasbg.fr/pub/ClustalX/ and
- ftp://ftp-igbmc.u-strasbg.fr/pub/ClustalW/
+Files: clustalw.1, clustalx.1
+Copyright: © 1998-1999 Stephane Bortzmeyer <bortzmeyer at debian.org>
+Licence: Unknown
-while the source was merged to one common upstream source (see README.Debian)
+Files: *
+Copyright: © Des Higgins, Julie Thompson and Toby Gibson
+Licence: Not for commercial use, No modification of the code.
+ Licensing ClustalW and ClustalX
+ .
+ Date:29 November 2007
+ .
+ The copyright for ClustalW and ClustalX is held by Des Higgins, Julie Thompson
+ and Toby Gibson
+ .
+ The binaries and source code are made available and can be distributed subject
+ to the following conditions:
+ .
+ Users are free to redistribute ClustalW or ClustalX in it's unmodified form as
+ long as it is not for commercial gain.
+ .
+ Anyone wishing to redistribute Clustal commercially should contact Toby Gibson
+ at gibson at embl.de
+ .
+ .
+ If users make changes/have ideas that they believe would be useful to the
+ broader research community they can send their suggestions to the clustal
+ development team at clustalw at ucd.ie where they will be considered for inclusion
+ in future releases.
-Authors:
-Toby Gibson <Toby.Gibson at EMBL-Heidelberg.de>
-Julie Thompson <julie at titus.u-strasbg.fr>
-Des Higgins <d.higgins at ucc.ie>
-
-Copyright:
-
-Non-free. You cannot distribute it at will.
-
-Debian holds a special exemption for distributing (see below). The licence does
-not forbid Debian from using autobuilders to create binary packages.
-
-Licence included here:
-
-**********************
-LICENCE FOR CLUSTAL W
-**********************
-
-Clustal W (hereafter "the program") is copyright (c) 1994-1998 by Julie D.
-Thompson, Desmond G. Higgins and Toby J. Gibson.
-
-Permission is granted to copy, distribute and use the program provided no fee
-is charged for it and provided that this copyright and licence notice is not
-removed or altered.
-
-The full source code of the program is provided free. You should not
-distribute a modified version of the program without obtaining the permission
-of the authors. You must keep the original copyright and licence notice. You
-must also document clearly the modifications you have made. You must make
-clear that this is not the original version.
-
-Commercial distributors of Clustal W are requested to contact the Clustal W
-authors in order to take out a non-exclusive licence. See the README file
-included with Clustal W for a rationale.
-
-You should understand that this software is provided as-is. The authors make
-no claims towards its suitability for any purpose and accept absolutely no
-liability for any damages the program may cause. Use at your own risk.
-
-* End of licence
-
-
-
-Special authorization for Debian:
-
-
-
-From: "Toby Gibson" <Toby.Gibson at EMBL-Heidelberg.de>
-Date: Thu, 17 Dec 1998 14:37:02 +0100
-To: Stephane Bortzmeyer <bortzmeyer at debian.org>
-Subject: Re: Fwd: clustalw_1.7-4_i386.changes REJECTED
-
-Hi Stephane,
-
-Now that we have thought about it, I don't think we can meet your stricter free
-criterion. There are already several companies who bundle Clustal W in sequence
-analysis packages and so are effectively selling it. They have paid for
-non-exclusive licences even though anyone can get the program for free: but
-they must have a multiple alignment engine, so we might as well earn some money
-which we can put toward further development.
-
-I think the main thing is to allow the distribution at all by Debian. We seem
-to have reached this point.
-
-Please do include this licence in the Debian package and I hope the release can
-go smoothly from now on.
+X-Comment: Frequently asked questions about Clustal licensing?
+ ---------------------------------------------------
+ .
+ 1. Do I have to pay to use ClustalW or ClustalX?
+ No - unless you wish to redistribute Clustal for profit. In this case see question 4.
+ .
+ 2. Can I redistribute the Clustal binaries and source code?
+ Yes. We have always wanted to see Clustal have as wide a userbase and
+ distribution network as possible and are happy to see other sites host copies
+ of the official Clustal code.
+ .
+ 3. Can I make changes to the source code?
+ .
+ You can make changes for your own purposes but you should not redistribute the
+ changed code.
+ .
+ 4. I want to include ClustalW/ClustalX in a commercial application who should I contact?
+ Toby Gibson at gibson at embl.de (also cc des.higgins at ucd.ie)
+ .
+ 5. There is no Clustal distribution for platform X. I have changed the code in
+ order to compile Clustal on this platform. Can I redistribute it?
+ .
+ Ideally you should send us a copy of your source code changes as well as a
+ binary. We will include it in our contributed binaries section on our FTP site
+ along with an acknowledgement of your contribution.
Modified: trunk/packages/clustalw/trunk/debian/rules
===================================================================
--- trunk/packages/clustalw/trunk/debian/rules 2008-01-15 20:04:31 UTC (rev 1145)
+++ trunk/packages/clustalw/trunk/debian/rules 2008-01-16 13:22:51 UTC (rev 1146)
@@ -1,45 +1,33 @@
#!/usr/bin/make -f
-# Uncomment this to turn on verbose mode.
-#export DH_VERBOSE=1
-
include /usr/share/quilt/quilt.make
-
-build: patch build-stamp
+build: build-stamp
build-stamp:
dh_testdir
-
+ qmake-qt4
$(MAKE)
-
+ mv clustalQtcurrent clustalx
touch build-stamp
-clean: unpatch
+clean:
dh_testdir
dh_testroot
- rm -f build-stamp
-
[ ! -f Makefile ] || $(MAKE) distclean
+ dh_clean build-stamp
- dh_clean
-
install:
install: build
dh_testdir
dh_testroot
dh_clean -k
dh_installdirs
-
- # Use dh_install instead of make install
- # $(MAKE) DESTDIR=`pwd`/debian/tmp install
-
dh_install
# Build architecture-dependent files here.
binary-arch: build install
dh_testdir
dh_testroot
-# dh_installdebconf
dh_installdocs
dh_installexamples
dh_installmenu
@@ -51,18 +39,12 @@
dh_link
dh_compress
dh_fixperms
-# dh_makeshlibs
dh_installdeb
-# dh_perl
dh_shlibdeps
dh_gencontrol
dh_md5sums
dh_builddeb
-get-orig-source:
- destdir=.;if [ -d debian ]; then destdir=..; fi; \
- lynx --dump ftp://ftp.ebi.ac.uk/pub/software/unix/clustalx/clustalx1.83.sun.tar.gz | tar --delete clustalx1.83.sun/clustalx clustalx1.83.sun/clustalw -f - | gzip -c > $$destdir/clustalw_1.83.orig.tar.gz
-
binary: binary-arch
binary-indep: # does nothing
.PHONY: build clean binary-arch binary install
Deleted: trunk/packages/clustalw/trunk/debian/shlibs.local
===================================================================
--- trunk/packages/clustalw/trunk/debian/shlibs.local 2008-01-15 20:04:31 UTC (rev 1145)
+++ trunk/packages/clustalw/trunk/debian/shlibs.local 2008-01-16 13:22:51 UTC (rev 1146)
@@ -1 +0,0 @@
-libXm 2 lesstif2 (>= 1:0.95.0-2.1)
Modified: trunk/packages/clustalw/trunk/debian/watch
===================================================================
--- trunk/packages/clustalw/trunk/debian/watch 2008-01-15 20:04:31 UTC (rev 1145)
+++ trunk/packages/clustalw/trunk/debian/watch 2008-01-16 13:22:51 UTC (rev 1146)
@@ -1,4 +1,2 @@
version=3
-ftp://ftp-igbmc.u-strasbg.fr/pub/ClustalW/clustalw(.*)\.linux\.tar\.gz
-# Alternative address
-#ftp://ftp.ebi.ac.uk/pub/software/unix/clustalw/clustalw(.*)\.linux\.tar\.gz
+ftp://ftp.ebi.ac.uk/pub/software/clustalw2/clustalx-src-([\d\.]+).zip
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