[med-svn] r1152 - in trunk/packages: . clustalw/trunk clustalw/trunk/debian clustalx/trunk clustalx/trunk/debian
charles-guest at alioth.debian.org
charles-guest at alioth.debian.org
Thu Jan 17 14:07:21 UTC 2008
Author: charles-guest
Date: 2008-01-17 14:07:17 +0000 (Thu, 17 Jan 2008)
New Revision: 1152
Added:
trunk/packages/clustalw/trunk/LICENSE
trunk/packages/clustalx/
trunk/packages/clustalx/trunk/LICENSE
Removed:
trunk/packages/clustalw/trunk/clustalx.1
trunk/packages/clustalw/trunk/debian/clustalx.desktop
trunk/packages/clustalw/trunk/debian/clustalx.dirs
trunk/packages/clustalw/trunk/debian/clustalx.docs
trunk/packages/clustalw/trunk/debian/clustalx.install
trunk/packages/clustalw/trunk/debian/clustalx.manpages
trunk/packages/clustalw/trunk/debian/clustalx.menu
trunk/packages/clustalw/trunk/debian/clustalx.mime
trunk/packages/clustalw/trunk/debian/clustalx.sharedmimeinfo
trunk/packages/clustalx/trunk/clustalw.1
trunk/packages/clustalx/trunk/debian/README.debian
trunk/packages/clustalx/trunk/debian/clustalw.docs
trunk/packages/clustalx/trunk/debian/clustalw.examples
trunk/packages/clustalx/trunk/debian/clustalw.install
trunk/packages/clustalx/trunk/debian/clustalw.manpages
trunk/packages/clustalx/trunk/debian/clustalw.menu
trunk/packages/clustalx/trunk/tests.clustalw/
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/control
trunk/packages/clustalw/trunk/debian/copyright
trunk/packages/clustalw/trunk/debian/rules
trunk/packages/clustalw/trunk/debian/watch
trunk/packages/clustalx/trunk/debian/changelog
trunk/packages/clustalx/trunk/debian/clustalx.docs
trunk/packages/clustalx/trunk/debian/control
trunk/packages/clustalx/trunk/debian/copyright
Log:
separating Clustal?\194?\160X and W
Added: trunk/packages/clustalw/trunk/LICENSE
===================================================================
--- trunk/packages/clustalw/trunk/LICENSE (rev 0)
+++ trunk/packages/clustalw/trunk/LICENSE 2008-01-17 14:07:17 UTC (rev 1152)
@@ -0,0 +1,34 @@
+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.
+
+
+
+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.
Deleted: trunk/packages/clustalw/trunk/clustalx.1
===================================================================
--- trunk/packages/clustalw/trunk/clustalx.1 2008-01-17 11:06:00 UTC (rev 1151)
+++ trunk/packages/clustalw/trunk/clustalx.1 2008-01-17 14:07:17 UTC (rev 1152)
@@ -1,38 +0,0 @@
-.TH CLUSTALW 1 "2003 July 1" "Manual for clustalw"
-.SH NAME
-clustalw \- a multiple sequence alignment program
-
-.SH SYNOPSIS
-.B clustalw
-.I "[options]"
-.SH "DESCRIPTION"
-This manual page documents briefly the
-.BR clustalx
-command.
-This manual page was written for the Debian GNU/Linux distribution
-because the original program does not have a manual page.
-Instead, it has other documentation; see below.
-.PP
-.B clustalx
-is a windows interface for the ClustalW multiple sequence alignment
-program. It provides an integrated environment for performing multiple sequence
-and profile alignments and analysing the results. The sequence alignment is
-displayed in a window on the screen. A versatile coloring scheme has been
-incorporated allowing you to highlight conserved features in the alignment.
-The pull-down menus at the top of the window allow you to select all the
-options required for traditional multiple sequence and profile alignment.
-.P
-You can cut-and-paste sequences to change the order of the alignment; you can
-select a subset of sequences to be aligned; you can select a sub-range of the
-alignment to be realigned and inserted back into the original alignment.
-.P
-Alignment quality analysis can be performed and low-scoring segments or
-exceptional residues can be highlighted.
-
-.SH "SEE ALSO"
-Files in /usr/share/doc/clustalx contain a lot
-of details. The Web page <http://www-igbmc.u-strasbg.fr/BioInfo/ClustalW/>
-is also helpful.
-.SH AUTHOR
-This manual page was written by Andreas Tille <tille at debian.org>,
-for the Debian GNU/Linux system (but may be used by others).
Modified: trunk/packages/clustalw/trunk/debian/changelog
===================================================================
--- trunk/packages/clustalw/trunk/debian/changelog 2008-01-17 11:06:00 UTC (rev 1151)
+++ trunk/packages/clustalw/trunk/debian/changelog 2008-01-17 14:07:17 UTC (rev 1152)
@@ -1,17 +1,12 @@
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.
- - text/x-clustalw-alignment associated to clustalx in clustalx.mime.
- - debian/rules calls dh_installmime.
+ * Clustal X is now built in a separate source package.
- -- Charles Plessy <charles-debian-nospam at plessy.org> Mon, 14 Jan 2008 19:15:13 +0900
+ -- Charles Plessy <charles-debian-nospam at plessy.org> Thu, 17 Jan 2008 23:00:28 +0900
clustalw (1.83-3) unstable; urgency=low
Modified: trunk/packages/clustalw/trunk/debian/clustalw.docs
===================================================================
--- trunk/packages/clustalw/trunk/debian/clustalw.docs 2008-01-17 11:06:00 UTC (rev 1151)
+++ trunk/packages/clustalw/trunk/debian/clustalw.docs 2008-01-17 14:07:17 UTC (rev 1152)
@@ -1 +1,2 @@
README
+LICENSE
Modified: trunk/packages/clustalw/trunk/debian/clustalw.install
===================================================================
--- trunk/packages/clustalw/trunk/debian/clustalw.install 2008-01-17 11:06:00 UTC (rev 1151)
+++ trunk/packages/clustalw/trunk/debian/clustalw.install 2008-01-17 14:07:17 UTC (rev 1152)
@@ -1,2 +1,2 @@
-#clustalw2.1/clustalw usr/bin
-clustalw2.1/clustalw_help usr/share/clustalw
+clustalw usr/bin
+clustalw_help usr/share/clustalw
Deleted: trunk/packages/clustalw/trunk/debian/clustalx.desktop
===================================================================
--- trunk/packages/clustalw/trunk/debian/clustalx.desktop 2008-01-17 11:06:00 UTC (rev 1151)
+++ trunk/packages/clustalw/trunk/debian/clustalx.desktop 2008-01-17 14:07:17 UTC (rev 1152)
@@ -1,17 +0,0 @@
-[Desktop Entry]
-Version=1.0
-Terminal=false
-Icon=clustalx
-Exec=clustalx
-Name=Clustal X
-GenericName=Alignment and phylogeny
-GenericName[en]=Alignment and phylogeny
-GenericName[fr]=Alignement et phylogénèse
-GenericName[pt_BR]=Alinhamento e filogenia
-Comment=Global multiple nucleotide or peptide sequence alignment and phyolgenetic analysis
-Comment[en]=Global multiple nucleotide or peptide sequence alignment and phylogenetic analysis
-Comment[fr]=Alignement global de séquences peptidiques ou nucléotidiques et analyse phylogénétique
-Comment[pt_BR]=Alinhamento global de sequências peptídicas ou nucleotídeos e análise filogenética
-Type=Application
-Categories=Biology;Science;Education;
-MimeType=text/x-clustalw-alignment;
Deleted: trunk/packages/clustalw/trunk/debian/clustalx.dirs
===================================================================
--- trunk/packages/clustalw/trunk/debian/clustalx.dirs 2008-01-17 11:06:00 UTC (rev 1151)
+++ trunk/packages/clustalw/trunk/debian/clustalx.dirs 2008-01-17 14:07:17 UTC (rev 1152)
@@ -1 +0,0 @@
-usr/share/applications
Deleted: trunk/packages/clustalw/trunk/debian/clustalx.docs
===================================================================
--- trunk/packages/clustalw/trunk/debian/clustalx.docs 2008-01-17 11:06:00 UTC (rev 1151)
+++ trunk/packages/clustalw/trunk/debian/clustalx.docs 2008-01-17 14:07:17 UTC (rev 1152)
@@ -1 +0,0 @@
-README
Deleted: trunk/packages/clustalw/trunk/debian/clustalx.install
===================================================================
--- trunk/packages/clustalw/trunk/debian/clustalx.install 2008-01-17 11:06:00 UTC (rev 1151)
+++ trunk/packages/clustalw/trunk/debian/clustalx.install 2008-01-17 14:07:17 UTC (rev 1152)
@@ -1,3 +0,0 @@
-clustalx usr/bin
-clustalx.hlp usr/share/clustalw
-debian/clustalx.desktop usr/share/applications
Deleted: trunk/packages/clustalw/trunk/debian/clustalx.manpages
===================================================================
--- trunk/packages/clustalw/trunk/debian/clustalx.manpages 2008-01-17 11:06:00 UTC (rev 1151)
+++ trunk/packages/clustalw/trunk/debian/clustalx.manpages 2008-01-17 14:07:17 UTC (rev 1152)
@@ -1 +0,0 @@
-clustalx.1
Deleted: trunk/packages/clustalw/trunk/debian/clustalx.menu
===================================================================
--- trunk/packages/clustalw/trunk/debian/clustalx.menu 2008-01-17 11:06:00 UTC (rev 1151)
+++ trunk/packages/clustalw/trunk/debian/clustalx.menu 2008-01-17 14:07:17 UTC (rev 1152)
@@ -1,5 +0,0 @@
-?package(clustalx):needs="X11" \
- section="Applications/Science/Biology" \
- title="ClustalX" \
- command="/usr/bin/clustalx"\
- hints="GUI for clustalw"
Deleted: trunk/packages/clustalw/trunk/debian/clustalx.mime
===================================================================
--- trunk/packages/clustalw/trunk/debian/clustalx.mime 2008-01-17 11:06:00 UTC (rev 1151)
+++ trunk/packages/clustalw/trunk/debian/clustalx.mime 2008-01-17 14:07:17 UTC (rev 1152)
@@ -1 +0,0 @@
-text/x-clustalw-alignment; clustalx '%s'; description=Clustal W multiple sequence alignment; nametemplate=%s.aln
Deleted: trunk/packages/clustalw/trunk/debian/clustalx.sharedmimeinfo
===================================================================
--- trunk/packages/clustalw/trunk/debian/clustalx.sharedmimeinfo 2008-01-17 11:06:00 UTC (rev 1151)
+++ trunk/packages/clustalw/trunk/debian/clustalx.sharedmimeinfo 2008-01-17 14:07:17 UTC (rev 1152)
@@ -1,12 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<mime-info xmlns='http://www.freedesktop.org/standards/shared-mime-info'>
- <mime-type type="text/x-clustalw-alignment">
- <sub-class-of type="text/plain"/>
- <comment>Multiple sequence alignment in Clustal W format</comment>
- <comment xml:lang="fr">Alignement multiple de séquences au format Clustal W</comment>
- <magic priority="50">
- <match type="string" offset="0" value="CLUSTAL"/>
- </magic>
- <glob pattern="*.aln"/>
- </mime-type>
-</mime-info>
Modified: trunk/packages/clustalw/trunk/debian/control
===================================================================
--- trunk/packages/clustalw/trunk/debian/control 2008-01-17 11:06:00 UTC (rev 1151)
+++ trunk/packages/clustalw/trunk/debian/control 2008-01-17 14:07:17 UTC (rev 1152)
@@ -4,7 +4,7 @@
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), libqt4-dev, quilt
+Build-Depends: debhelper (>= 5), 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
@@ -33,30 +33,5 @@
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.
.
- For details and citation purposes see paper "Clustal W and Clustal X version
+ 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}
-Suggests: clustalw, texshade|texlive-latex-extra, boxshade
-Description: GUI for clustalw
- 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.
- A versatile coloring scheme has been incorporated to highlight conserved
- features in the alignment. For professional presentations, one should
- use the texshade LaTeX package or boxshade.
- .
- The pull-down menus at the top of the window allow you to select all the
- options required for traditional multiple sequence and profile alignment.
- You can cut-and-paste sequences to change the order of the alignment; you can
- select a subset of sequences to be aligned; you can select a sub-range of the
- alignment to be realigned and inserted back into the original alignment.
- .
- An alignment quality analysis can be performed and low-scoring segments or
- exceptional residues can be highlighted.
- .
- 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 2008-01-17 11:06:00 UTC (rev 1151)
+++ trunk/packages/clustalw/trunk/debian/copyright 2008-01-17 14:07:17 UTC (rev 1152)
@@ -19,7 +19,7 @@
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.
-Files: clustalw.1, clustalx.1
+Files: clustalw.1
Copyright: © 1998-1999 Stephane Bortzmeyer <bortzmeyer at debian.org>
Licence: Unknown
Modified: trunk/packages/clustalw/trunk/debian/rules
===================================================================
--- trunk/packages/clustalw/trunk/debian/rules 2008-01-17 11:06:00 UTC (rev 1151)
+++ trunk/packages/clustalw/trunk/debian/rules 2008-01-17 14:07:17 UTC (rev 1152)
@@ -5,9 +5,7 @@
build: build-stamp
build-stamp:
dh_testdir
- qmake-qt4
$(MAKE)
- mv clustalQtcurrent clustalx
touch build-stamp
clean:
Modified: trunk/packages/clustalw/trunk/debian/watch
===================================================================
--- trunk/packages/clustalw/trunk/debian/watch 2008-01-17 11:06:00 UTC (rev 1151)
+++ trunk/packages/clustalw/trunk/debian/watch 2008-01-17 14:07:17 UTC (rev 1152)
@@ -1,2 +1,2 @@
version=3
-ftp://ftp.ebi.ac.uk/pub/software/clustalw2/clustalx-src-([\d\.]+).zip
+ftp://ftp.ebi.ac.uk/pub/software/clustalw2/clustalw-linux-src-([\d\.]+).tar.gz
Copied: trunk/packages/clustalx (from rev 1151, trunk/packages/clustalw)
Added: trunk/packages/clustalx/trunk/LICENSE
===================================================================
--- trunk/packages/clustalx/trunk/LICENSE (rev 0)
+++ trunk/packages/clustalx/trunk/LICENSE 2008-01-17 14:07:17 UTC (rev 1152)
@@ -0,0 +1,34 @@
+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.
+
+
+
+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.
Deleted: trunk/packages/clustalx/trunk/clustalw.1
===================================================================
--- trunk/packages/clustalw/trunk/clustalw.1 2008-01-17 11:06:00 UTC (rev 1151)
+++ trunk/packages/clustalx/trunk/clustalw.1 2008-01-17 14:07:17 UTC (rev 1152)
@@ -1,56 +0,0 @@
-.TH CLUSTALW 1
-.\" NAME should be all caps, SECTION should be 1-8, maybe w/ subsection
-.\" other parms are allowed: see man(7), man(1)
-.SH NAME
-clustalw \- a multiple sequence alignment program
-
-.SH SYNOPSIS
-.B clustalw
-.I "[options]"
-.SH "DESCRIPTION"
-This manual page documents briefly the
-.BR clustalw
-command.
-This manual page was written for the Debian GNU/Linux distribution
-because the original program does not have a manual page.
-Instead, it has other documentation; see below.
-.PP
-.B clustalw
-is a program which performs
-simultaneous alignment of many nucleotide or amino acid sequences.
-It is typically run interactively, providing a menu and an online help.
-If you prefer to use it in command-line (batch) mode, you will have
-to give several options, the minimum being \-infile.
-.SH OPTIONS
-A summary of options are included below.
-For a complete description, see the last section.
-.TP
-.B \-infile=string
-Tells ClustalW to get input from the named file.
-Several formats are automatically recognized.
-.TP
-.B \-outfile=string
-Tells ClustalW to write output in the named file.
-.TP
-.B \-tree
-Calculates NJ tree.
-.TP
-.B \-profile
-Merges two alignments by profile alignment.
-.TP
-.B \-output=string
-Sets the output format. It can be GCG, GDE, PHYLIP or PIR.
-.TP
-.B \-quicktree
-Uses FAST algorithm for the alignment guide tree.
-.TP
-.B \-help
-Prints a short help. Warning: the syntax of the options is the VMS one. For
-Unix, change the / to a - and type the option name in lower case.
-.SH "SEE ALSO"
-The \-help option is a good summary. Files in /usr/share/doc/clustalw contains a lot
-of details. The Web page <http://www-igbmc.u-strasbg.fr/BioInfo/ClustalW/>
-is also helpful.
-.SH AUTHOR
-This manual page was written by Stephane Bortzmeyer <bortzmeyer at debian.org>,
-for the Debian GNU/Linux system (but may be used by others).
Deleted: trunk/packages/clustalx/trunk/debian/README.debian
===================================================================
--- trunk/packages/clustalw/trunk/debian/README.debian 2008-01-17 11:06:00 UTC (rev 1151)
+++ trunk/packages/clustalx/trunk/debian/README.debian 2008-01-17 14:07:17 UTC (rev 1152)
@@ -1,39 +0,0 @@
-ClustalW for DEBIAN
--------------------
-
-Comments regarding the Package
-
-I decided to continue packaging the program which was orphaned because
-I needed it for packageing Arb.
-
-I removed the binary versions of njplot inside the source package because
-they just bloat the source file with unused stuff.
-Moreover I included some documentation of the clustalx GUI from version
-1.81 and builded clustalx in an extra package.
-
-For further information you might read
- http://bioinformatics.org/software/mollin_entry.php3?name=clustalw
-
-Please report any problem with the package to the Debian bug tracking
-system.
-
-Andreas Tille <tille at debian.org>, Mon, 29 Oct 2001 21:40:20 +0100
-
-
-I am assisting Andreas in getting a new upstream version into Debian.
-ClustalX is apparently a superset of the source of ClustalW. However,
-to our surprise it is only distributed together with a binary. The
-source of ClustalW is distributed without binaries, but does not
-contain extras for ClustalX.
-
-In violation of the Debian Policy we therefore decided to remove the
-binaries from the ClustalX distribution (we chose the binaries for Sun
-just by chance) and refer to the remaining source code as the original
-distribution.
-
-Earlier maintainers seem to already have supported the concept of such a
-"virtual" original tar file. The debian/rules provide the get-orig-source
-script for an automated creation of the tar file as used for the diff.
-
-Steffen Moeller <moeller at pzr.uni-rostock.de> Mon, 30 Jun 2003 21:08:02 +0100
-
Modified: trunk/packages/clustalx/trunk/debian/changelog
===================================================================
--- trunk/packages/clustalw/trunk/debian/changelog 2008-01-17 11:06:00 UTC (rev 1151)
+++ trunk/packages/clustalx/trunk/debian/changelog 2008-01-17 14:07:17 UTC (rev 1152)
@@ -1,4 +1,4 @@
-clustalw (2.0-1) UNRELEASED; urgency=low
+clustalx (2.0-1) UNRELEASED; urgency=low
* New upstream release:
- Uses Qt instead of lesstif.
@@ -11,7 +11,7 @@
- text/x-clustalw-alignment associated to clustalx in clustalx.mime.
- debian/rules calls dh_installmime.
- -- Charles Plessy <charles-debian-nospam at plessy.org> Mon, 14 Jan 2008 19:15:13 +0900
+ -- Charles Plessy <charles-debian-nospam at plessy.org> Thu, 17 Jan 2008 22:55:41 +0900
clustalw (1.83-3) unstable; urgency=low
Deleted: trunk/packages/clustalx/trunk/debian/clustalw.docs
===================================================================
--- trunk/packages/clustalw/trunk/debian/clustalw.docs 2008-01-17 11:06:00 UTC (rev 1151)
+++ trunk/packages/clustalx/trunk/debian/clustalw.docs 2008-01-17 14:07:17 UTC (rev 1152)
@@ -1 +0,0 @@
-README
Deleted: trunk/packages/clustalx/trunk/debian/clustalw.examples
===================================================================
--- trunk/packages/clustalw/trunk/debian/clustalw.examples 2008-01-17 11:06:00 UTC (rev 1151)
+++ trunk/packages/clustalx/trunk/debian/clustalw.examples 2008-01-17 14:07:17 UTC (rev 1152)
@@ -1 +0,0 @@
-tests.clustalw
Deleted: trunk/packages/clustalx/trunk/debian/clustalw.install
===================================================================
--- trunk/packages/clustalw/trunk/debian/clustalw.install 2008-01-17 11:06:00 UTC (rev 1151)
+++ trunk/packages/clustalx/trunk/debian/clustalw.install 2008-01-17 14:07:17 UTC (rev 1152)
@@ -1,2 +0,0 @@
-#clustalw2.1/clustalw usr/bin
-clustalw2.1/clustalw_help usr/share/clustalw
Deleted: trunk/packages/clustalx/trunk/debian/clustalw.manpages
===================================================================
--- trunk/packages/clustalw/trunk/debian/clustalw.manpages 2008-01-17 11:06:00 UTC (rev 1151)
+++ trunk/packages/clustalx/trunk/debian/clustalw.manpages 2008-01-17 14:07:17 UTC (rev 1152)
@@ -1 +0,0 @@
-clustalw.1
Deleted: trunk/packages/clustalx/trunk/debian/clustalw.menu
===================================================================
--- trunk/packages/clustalw/trunk/debian/clustalw.menu 2008-01-17 11:06:00 UTC (rev 1151)
+++ trunk/packages/clustalx/trunk/debian/clustalw.menu 2008-01-17 14:07:17 UTC (rev 1152)
@@ -1,5 +0,0 @@
-?package(clustalw):needs="text"\
- section="Applications/Science/Biology"\
- title="ClustalW"\
- command="/usr/bin/clustalw"\
- hints="Global multiple nucleotide or peptide sequence alignment"
Modified: trunk/packages/clustalx/trunk/debian/clustalx.docs
===================================================================
--- trunk/packages/clustalw/trunk/debian/clustalx.docs 2008-01-17 11:06:00 UTC (rev 1151)
+++ trunk/packages/clustalx/trunk/debian/clustalx.docs 2008-01-17 14:07:17 UTC (rev 1152)
@@ -1 +1,2 @@
README
+LICENSE
Modified: trunk/packages/clustalx/trunk/debian/control
===================================================================
--- trunk/packages/clustalw/trunk/debian/control 2008-01-17 11:06:00 UTC (rev 1151)
+++ trunk/packages/clustalx/trunk/debian/control 2008-01-17 14:07:17 UTC (rev 1152)
@@ -1,4 +1,4 @@
-Source: clustalw
+Source: clustalx
Section: non-free/science
Priority: optional
Maintainer: Debian-Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
@@ -6,36 +6,11 @@
Uploaders: Steffen Moeller <moeller at debian.org>, Charles Plessy <charles-debian-nospam at plessy.org>
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
+Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/clustalx/trunk/
+Vcs-Svn: svn://svn.debian.org/svn/debian-med/trunk/packages/clustalx
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. 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 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.
- .
- 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}
@@ -58,5 +33,5 @@
An alignment quality analysis can be performed and low-scoring segments or
exceptional residues can be highlighted.
.
- For details and citation purposes see paper "Clustal W and Clustal X version
+ 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/clustalx/trunk/debian/copyright
===================================================================
--- trunk/packages/clustalw/trunk/debian/copyright 2008-01-17 11:06:00 UTC (rev 1151)
+++ trunk/packages/clustalx/trunk/debian/copyright 2008-01-17 14:07:17 UTC (rev 1152)
@@ -19,7 +19,7 @@
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.
-Files: clustalw.1, clustalx.1
+Files: clustalx.1
Copyright: © 1998-1999 Stephane Bortzmeyer <bortzmeyer at debian.org>
Licence: Unknown
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