[med-svn] r1409 - in trunk/packages/clustalw/trunk: . debian
smoe-guest at alioth.debian.org
smoe-guest at alioth.debian.org
Sun Feb 17 14:50:23 UTC 2008
Author: smoe-guest
Date: 2008-02-17 14:50:22 +0000 (Sun, 17 Feb 2008)
New Revision: 1409
Added:
trunk/packages/clustalw/trunk/CHANGELOG
trunk/packages/clustalw/trunk/debian/clustalw.1
Removed:
trunk/packages/clustalw/trunk/LICENSE
trunk/packages/clustalw/trunk/README
trunk/packages/clustalw/trunk/clustalw.1
Modified:
trunk/packages/clustalw/trunk/debian/README.debian
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/clustalw.manpages
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:
Except for some smallish lintian warnings, this package should be functional.
Added: trunk/packages/clustalw/trunk/CHANGELOG
===================================================================
--- trunk/packages/clustalw/trunk/CHANGELOG (rev 0)
+++ trunk/packages/clustalw/trunk/CHANGELOG 2008-02-17 14:50:22 UTC (rev 1409)
@@ -0,0 +1,59 @@
+* Added LICENSE file to distribution
+This file contains the information about commercial licensing of clustal as well as FAQ for licensing issues
+
+* Added README file to distribution
+This is the file that lists the files and directories on the Clustal FTP site.
+It also includes acknowledgements of people who have contributed binaries
+
+* Removed .pro Qt file from the distribution
+pro-file should be generated anew using qmake and modified according
+to build requirements, i.e. no need for version control.
+
+* Fixed bug where ClustalX2 was not processing command line args
+
+* Fixed Segfault on opening helpfile. Happened on Linux only with -O2
+and when calling binary directly, not using the wrapper
+
+* Added debian packaging files
+
+* Added support for help command line flag GUI/xmenus version
+When requesting help file, graphical version of command line help is
+displayed (1.83 tried to open clustalw help)
+
+* Added complete automake (configure etc) system according to the
+following websites:
+- http://www.openismus.com/documents/linux/automake/automake.shtml
+- http://www.bioinf.uni-freiburg.de/~mmann/HowTo/automake.html
+
+* clustalw files source files have been move to subdir
+
+* Fixed bug #53 change MAXNAMESTODISPLAY back to 10 from 30. This fixes problem of large amount of space between
+sequence name and actual alignment in clustal output files
+
+* This solves bug #72 with long lines (5000+) in fasta files
+changed code to use strings rather than arrays.
+Needed to add delim parameter to getline in order to read files formatted for different OSs on different platforms.
+
+* Fixed Bug 79:
+"The count of amino acids in the ClustalX Postscript output not correct"
+Off-by-one issue
+
+* ClustalX and ClustalW version numbers are now the same and defined in
+ClustalW code (automake)
+
+* Fixed problem with compilation of ClustalX2 with gcc3
+avoiding gcc3 error message: cannot declare member function
+QDir::currentPath'
+
+* Target now clustalw2 instead of clustalw
+
+* Fixed Bug 46
+added in aminoacid code O for pyrrolysine
+
+* Fixed bug 89
+changed clustalw2.0 to conform to 1.83 behaviour for width of sequence ID and
+alignment
+
+* Fixed bug 90
+changed clustalw2.0 to conform to 1.83 behaviour leading spaces are stripped
+from FASTA identifiers.
Deleted: trunk/packages/clustalw/trunk/LICENSE
===================================================================
--- trunk/packages/clustalw/trunk/LICENSE 2008-02-17 13:31:04 UTC (rev 1408)
+++ trunk/packages/clustalw/trunk/LICENSE 2008-02-17 14:50:22 UTC (rev 1409)
@@ -1,34 +0,0 @@
-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/README
===================================================================
--- trunk/packages/clustalw/trunk/README 2008-02-17 13:31:04 UTC (rev 1408)
+++ trunk/packages/clustalw/trunk/README 2008-02-17 14:50:22 UTC (rev 1409)
@@ -1,72 +0,0 @@
-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
Deleted: trunk/packages/clustalw/trunk/clustalw.1
===================================================================
--- trunk/packages/clustalw/trunk/clustalw.1 2008-02-17 13:31:04 UTC (rev 1408)
+++ trunk/packages/clustalw/trunk/clustalw.1 2008-02-17 14:50:22 UTC (rev 1409)
@@ -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).
Modified: trunk/packages/clustalw/trunk/debian/README.debian
===================================================================
--- trunk/packages/clustalw/trunk/debian/README.debian 2008-02-17 13:31:04 UTC (rev 1408)
+++ trunk/packages/clustalw/trunk/debian/README.debian 2008-02-17 14:50:22 UTC (rev 1409)
@@ -1,39 +1,15 @@
ClustalW for DEBIAN
-------------------
-Comments regarding the Package
+The packaging of ClustalW and ClustalX was recently split to better
+reflect the handling of upstream and thus reduce our effort. The name of
+the binary remains clustalw instead of upstream's clustalw2. If there
+are any problems with this approeach, then please inform us about it.
+At the moment, there can only be one installation of ClustalW at a time.
+This may be disadvantageous to those who aim at comparing multiple
+version. But for these rather exceptional cases it may be appropriate
+to install chroot environments.
-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
+Steffen Moeller <moeller at debian.org> Sun, 17 Feb 2008 15:43:42 +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/clustalw/trunk/debian/changelog
===================================================================
--- trunk/packages/clustalw/trunk/debian/changelog 2008-02-17 13:31:04 UTC (rev 1408)
+++ trunk/packages/clustalw/trunk/debian/changelog 2008-02-17 14:50:22 UTC (rev 1409)
@@ -1,3 +1,15 @@
+clustalw (2.0.1-1) UNRELEASED; urgency=low
+
+ [ Steffen Moeller ]
+ * New upstream release
+ * updated debian/watch
+ * moved clustalw.1 into debian folder (easier to work
+ with svn-buildpackage)
+ * removed README and LICENSE from svn since these are
+ now distributed with the upstream sources
+
+ -- Steffen Moeller <moeller at debian.org> Sun, 17 Feb 2008 15:18:34 +0100
+
clustalw (2.0-1) UNRELEASED; urgency=low
[ Charles Plessy ]
Copied: trunk/packages/clustalw/trunk/debian/clustalw.1 (from rev 1386, trunk/packages/clustalw/trunk/clustalw.1)
===================================================================
--- trunk/packages/clustalw/trunk/debian/clustalw.1 (rev 0)
+++ trunk/packages/clustalw/trunk/debian/clustalw.1 2008-02-17 14:50:22 UTC (rev 1409)
@@ -0,0 +1,56 @@
+.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).
Modified: trunk/packages/clustalw/trunk/debian/clustalw.docs
===================================================================
--- trunk/packages/clustalw/trunk/debian/clustalw.docs 2008-02-17 13:31:04 UTC (rev 1408)
+++ trunk/packages/clustalw/trunk/debian/clustalw.docs 2008-02-17 14:50:22 UTC (rev 1409)
@@ -1,2 +1 @@
README
-LICENSE
Modified: trunk/packages/clustalw/trunk/debian/clustalw.install
===================================================================
--- trunk/packages/clustalw/trunk/debian/clustalw.install 2008-02-17 13:31:04 UTC (rev 1408)
+++ trunk/packages/clustalw/trunk/debian/clustalw.install 2008-02-17 14:50:22 UTC (rev 1409)
@@ -1,2 +1 @@
-clustalw usr/bin
clustalw_help usr/share/clustalw
Modified: trunk/packages/clustalw/trunk/debian/clustalw.manpages
===================================================================
--- trunk/packages/clustalw/trunk/debian/clustalw.manpages 2008-02-17 13:31:04 UTC (rev 1408)
+++ trunk/packages/clustalw/trunk/debian/clustalw.manpages 2008-02-17 14:50:22 UTC (rev 1409)
@@ -1 +1 @@
-clustalw.1
+debian/clustalw.1
Modified: trunk/packages/clustalw/trunk/debian/control
===================================================================
--- trunk/packages/clustalw/trunk/debian/control 2008-02-17 13:31:04 UTC (rev 1408)
+++ trunk/packages/clustalw/trunk/debian/control 2008-02-17 14:50:22 UTC (rev 1409)
@@ -16,7 +16,7 @@
Depends: ${shlibs:Depends}
Suggests: clustalx, seaview
Enhances: t-coffee
-Description: Global multiple nucleotide or peptide sequence alignment
+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
Modified: trunk/packages/clustalw/trunk/debian/copyright
===================================================================
--- trunk/packages/clustalw/trunk/debian/copyright 2008-02-17 13:31:04 UTC (rev 1408)
+++ trunk/packages/clustalw/trunk/debian/copyright 2008-02-17 14:50:22 UTC (rev 1409)
@@ -17,9 +17,9 @@
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.
+ of Charles Plessy and Steffen Möller can be treated as if it were public domain.
-Files: clustalw.1
+Files: debian/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 2008-02-17 13:31:04 UTC (rev 1408)
+++ trunk/packages/clustalw/trunk/debian/rules 2008-02-17 14:50:22 UTC (rev 1409)
@@ -2,8 +2,13 @@
include /usr/share/quilt/quilt.make
+configure-stamp: config.status
+config.status:
+ ./configure --prefix=/usr
+ touch configure-stamp
+
build: build-stamp
-build-stamp:
+build-stamp: configure-stamp
dh_testdir
$(MAKE)
touch build-stamp
@@ -20,6 +25,9 @@
dh_testroot
dh_clean -k
dh_installdirs
+ # could anyone fix this and send this to upstream, please?
+ #$(MAKE) PREFIX=$(CURDIR)/debian/clustalw/usr install
+ cp src/clustalw2 $(CURDIR)/debian/clustalw/usr/bin/clustalw
dh_install
# Build architecture-dependent files here.
@@ -27,7 +35,11 @@
dh_testdir
dh_testroot
dh_installdocs
- dh_installexamples
+ @if [ -d tests.clustalw ]; then \
+ dh_installexamples; \
+ else \
+ echo "** Could not find folder with examples - you are just testing, right? **"; \
+ fi
dh_installmenu
dh_desktop
dh_installmime
Modified: trunk/packages/clustalw/trunk/debian/watch
===================================================================
--- trunk/packages/clustalw/trunk/debian/watch 2008-02-17 13:31:04 UTC (rev 1408)
+++ trunk/packages/clustalw/trunk/debian/watch 2008-02-17 14:50:22 UTC (rev 1409)
@@ -1,2 +1,3 @@
version=3
-ftp://ftp.ebi.ac.uk/pub/software/clustalw2/clustalw-linux-src-([\d\.]+).tar.gz
+ftp://ftp.ebi.ac.uk/pub/software/clustalw2/clustalw-(.*)-src.tar.gz
+
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