[med-svn] r1094 - in trunk/packages: . mustang mustang/trunk mustang/trunk/debian mustang/trunk/debian/patches
tille at alioth.debian.org
tille at alioth.debian.org
Thu Jan 10 15:46:49 UTC 2008
Author: tille
Date: 2008-01-10 15:46:49 +0000 (Thu, 10 Jan 2008)
New Revision: 1094
Added:
trunk/packages/mustang/
trunk/packages/mustang/trunk/
trunk/packages/mustang/trunk/debian/
trunk/packages/mustang/trunk/debian/changelog
trunk/packages/mustang/trunk/debian/compat
trunk/packages/mustang/trunk/debian/control
trunk/packages/mustang/trunk/debian/copyright
trunk/packages/mustang/trunk/debian/mustang.1
trunk/packages/mustang/trunk/debian/mustang.manpages
trunk/packages/mustang/trunk/debian/patches/
trunk/packages/mustang/trunk/debian/patches/00list
trunk/packages/mustang/trunk/debian/patches/main.cpp.dpatch
trunk/packages/mustang/trunk/debian/patches/test_zf-cchh.dpatch
trunk/packages/mustang/trunk/debian/rules
trunk/packages/mustang/trunk/debian/runtest
Log:
Added mustang to svn
Added: trunk/packages/mustang/trunk/debian/changelog
===================================================================
--- trunk/packages/mustang/trunk/debian/changelog (rev 0)
+++ trunk/packages/mustang/trunk/debian/changelog 2008-01-10 15:46:49 UTC (rev 1094)
@@ -0,0 +1,28 @@
+mustang (3.0-1) unstable; urgency=low
+
+ * Upload mustang to Debian (Closes: #459637).
+ * debian/control: Maintainer and homepage fields set as per
+ Debian policy.
+ * debian/rules: add get-orig-source target.
+
+ -- Morten Kjeldgaard <mok at bioxray.dk> Mon, 07 Jan 2008 13:44:36 +0100
+
+mustang (3.0-0ubuntu1) gutsy; urgency=low
+
+ * Initial release
+ * Manpage mustang.1 authored from information in the README.txt file.
+ * The upstream tarball was repackaged to remove PDB files which have an
+ undetermined copyright status and hence can not be distributed.
+ Furthermore, the license was extracted from one of the source files
+ and placed in the file 'LICENSE'. A note describing the repackaging in
+ detail is placed in debian/copyright.
+ * Instead of the PDB files included in the original tarball, a script is
+ supplied that allows the user to fetch a few PDB files and test that
+ mustang works.
+ * A patch on main.cpp is supplied to beautify the output of the initial
+ author blurb. The tabs in the output were removed to make the output
+ easier to read in a default 80 columns wide terminal window.
+
+ -- Morten Kjeldgaard <mok at bioxray.dk> Mon, 25 Jun 2007 15:55:12 +0000
+
+
Added: trunk/packages/mustang/trunk/debian/compat
===================================================================
--- trunk/packages/mustang/trunk/debian/compat (rev 0)
+++ trunk/packages/mustang/trunk/debian/compat 2008-01-10 15:46:49 UTC (rev 1094)
@@ -0,0 +1 @@
+5
Added: trunk/packages/mustang/trunk/debian/control
===================================================================
--- trunk/packages/mustang/trunk/debian/control (rev 0)
+++ trunk/packages/mustang/trunk/debian/control 2008-01-10 15:46:49 UTC (rev 1094)
@@ -0,0 +1,18 @@
+Source: mustang
+Section: science
+Priority: optional
+Maintainer: Morten Kjeldgaard <mok at bioxray.dk>
+Homepage: http://www.cs.mu.oz.au/~arun/mustang/
+Build-Depends: debhelper (>= 5), dpatch
+Standards-Version: 3.7.3
+
+Package: mustang
+Architecture: any
+Depends: ${shlibs:Depends}
+Description: multiple structural alignment of proteins
+ Mustang is an algorithm for structural alignment of multiple
+ protein structures. Given a set of PDB files, the program uses the spatial
+ information in the Calpha atoms of the set to produce a sequence alignment.
+ Based on a progressive pairwise heuristic the algorithm then proceeds
+ through a number of refinement passes. Mustang reports the multiple
+ sequence alignment and the corresponding superposition of structures.
Added: trunk/packages/mustang/trunk/debian/copyright
===================================================================
--- trunk/packages/mustang/trunk/debian/copyright (rev 0)
+++ trunk/packages/mustang/trunk/debian/copyright 2008-01-10 15:46:49 UTC (rev 1094)
@@ -0,0 +1,66 @@
+This package was debianized by Morten Kjeldgaard <mok at bioxray.dk> on
+Wed, 6 Jun 2007 22:32:12 +0000.
+
+It was downloaded from http://www.cs.mu.oz.au/~arun/mustang/
+
+Upstream Author: Arun S. Konagurthu <arun at bx.psu.edu>
+ homepage: http://www.bx.psu.edu/arun
+
+Copyright: Copyright (c) 2005, Arun S Konagurthu,
+ The University of Melbourne. All rights reserved.
+
+License:
+
+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.
+
+* Neither the name of the University of Melbourne nor the names of its
+ contributors may be used to endorse or promote products derived from this
+ software without specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "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 COPYRIGHT OWNER OR CONTRIBUTORS 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.
+
+
+Debian packaging
+================
+
+Copyright of the Debian packaging is assigned to the copyright holder and
+condition to the above license.
+
+
+Repackaging of the original tarball
+===================================
+
+The upstream tarball was repackaged to remove PDB files which have an
+undetermined copyright status and hence cannot be distributed. Furthermore,
+the text of the license was added in the top level directory in the file
+`LICENSE'.
+
+The repackaging can be reproduced by running the following script:
+
+wget http://www.cs.mu.oz.au/~arun/mustang/mustang_v.3.tgz
+
+tar -xf mustang_v.3.tgz
+mv MUSTANG_v.3/ mustang-3.0.orig
+rm -rf mustang-3.0.orig/data/test/pdbs
+
+head -21 mustang-3.0.orig/src/main.cpp |tail -20 > mustang-3.0.orig/LICENSE
+tar -czf mustang_3.0.orig.tar.gz mustang-3.0.orig
+
Added: trunk/packages/mustang/trunk/debian/mustang.1
===================================================================
--- trunk/packages/mustang/trunk/debian/mustang.1 (rev 0)
+++ trunk/packages/mustang/trunk/debian/mustang.1 2008-01-10 15:46:49 UTC (rev 1094)
@@ -0,0 +1,90 @@
+.\" Hey, EMACS: -*- mode: nroff; mode:font-lock -*-
+.TH MUSTANG 1 "June 6, 2007"
+.\" Please adjust this date whenever revising the manpage.
+.\"
+.SH NAME
+mustang \- a multiple structural alignment algorithm
+.SH SYNOPSIS
+.B mustang
+.RI [ options ] " files" ...
+.SH DESCRIPTION
+This manual page documents briefly the \fBmustang\fR command.
+
+\fBMustang\fR is a program that implements an algorithm for structural
+alignment of multiple protein structures. Given a set of PDB files, the
+program uses the spatial information in the Calpha atoms of the set to
+produce a sequence alignment. Based on a progressive pairwise heuristic
+the algorithm then proceeds through a number of refinement
+passes. \fBMustang\fR reports the multiple sequence alignment and the
+corresponding superposition of structures.
+
+To keep the command line short the user can write the path and file names
+into a (description) file and supply the description file at the command
+line using the '\-f' option. For example see the file used to test the
+installation: '/usr/share/doc/mustang/examples/test_zf\-CCHH'.
+
+PATH should have a prefix '>'. When the program parses this file, it looks
+for the line starting with '>' symbol (whitespaces are ignored before and
+after the symbol). The PATH containing the PDB files of the structures to
+be aligned should follow. See for example: /usr/share/doc/mustang/examples/test_zf\-CCHH'.
+
+FILENAMES should have a prefix '+' (whitespaces are ignored before and
+after this symbol). If PATH is specified then only the filenames should be
+provided after the '+' symbol. However, if PATH line is NOT provided, then
+the absolute/relative paths of the structure files should be provided.
+
+The description file format is described further under the \fB\-f\fP CmdLine
+option).
+.SH OPTIONS
+A summary of options is included below.
+.TP
+.BI \-p " <path>"
+Path to the directory holding the (PDB) structures
+to be aligned.
+.TP
+.BI \-i " <struct\-1> <struct\-2>" ...
+Input structures to be aligned. Note: if \fB\-p\fR option is used in the
+command line, supply only the file names of the structures; if not give the
+absolute/relative path of each of the input structures.
+.TP
+.BI \-f " <description file>"
+This option is used to AVOID entering the path (\fB\-p\fR) and file name
+(\fB\-i\fR) details in the command line. Instead, to keep the command line
+short, the user can enter the path and file name details in a "description"
+file and supply it in the command line. The format of the "description
+file" is furher discussed in the 'DESCRIPTION' section above. Note: the
+options { \fB\-p\fR , \fB\-i\fR} and {\fB\-f\fR} are mutually exclusive.
+.TP
+.BI \-o " <output identifier>"
+A common identifier for various outputs of the program. Appropriate
+extentions (e.g. \fI<identifier>\fR.html, \fI<identifier>\fR.pdb,
+\fI<identifier>\fR.msf) will be added to this identifier depending on the
+options the user specifies in the command line.
+DEFAULT output identifier: 'results'
+.TP
+.BI \-F " <fmt>"
+Alignment output format. The choices for \fI<fmt>\fR are: 'html', 'fasta',
+ 'pir', 'msf'. DEFAULT format: 'html'
+.TP
+.BI \-D " [CA\-CA diameter]"
+Produce an HTML file where the the residues are reported in lower case with
+grey background when the aligned(superposed) CA\-CA diamter of residues in a
+column of alignment is > the CA\-CA diameter threshold.
+.TP
+.BI \-s " [<ON>/<OFF>]"
+Generate a PDB file containing optimal superposition of all the structures
+based on the alignment. DEFAULT: 'ON'.
+.TP
+.B \-\-help
+display a help message and exits.
+.TP
+.B \-\-version
+output version information and exits.
+
+.SH AUTHORS
+\fBMustang\fR was written by A. S. Konagurthu, using an algorithm from
+A. S. Konagurthu, J. Whisstock, P. J. Stuckey, and A. M. Lesk.
+.PP
+This manual page was written by Morten Kjeldgaard <mok at bioxray.dk>.
+.SH SEE ALSO
+\fBMustang\fR's homepage: http://www.cs.mu.oz.au/~arun/mustang/
Added: trunk/packages/mustang/trunk/debian/mustang.manpages
===================================================================
--- trunk/packages/mustang/trunk/debian/mustang.manpages (rev 0)
+++ trunk/packages/mustang/trunk/debian/mustang.manpages 2008-01-10 15:46:49 UTC (rev 1094)
@@ -0,0 +1 @@
+debian/mustang.1
Added: trunk/packages/mustang/trunk/debian/patches/00list
===================================================================
--- trunk/packages/mustang/trunk/debian/patches/00list (rev 0)
+++ trunk/packages/mustang/trunk/debian/patches/00list 2008-01-10 15:46:49 UTC (rev 1094)
@@ -0,0 +1,2 @@
+test_zf-cchh.dpatch
+main.cpp.dpatch
Added: trunk/packages/mustang/trunk/debian/patches/main.cpp.dpatch
===================================================================
--- trunk/packages/mustang/trunk/debian/patches/main.cpp.dpatch (rev 0)
+++ trunk/packages/mustang/trunk/debian/patches/main.cpp.dpatch 2008-01-10 15:46:49 UTC (rev 1094)
@@ -0,0 +1,34 @@
+#! /bin/sh /usr/share/dpatch/dpatch-run
+## main.cpp.dpatch by Morten Kjeldgaard <mok at bioxray.dk>
+##
+## All lines beginning with `## DP:' are a description of the patch.
+## DP: beautify output of initial advertisement
+
+ at DPATCH@
+
+--- mustang-3.0/src/main.cpp 2006-10-19 18:39:45.000000000 +0200
++++ mustang-3.0.orig/src/main.cpp 2007-08-22 17:13:17.000000000 +0200
+@@ -64,17 +64,17 @@
+ if(!meditate)
+ {
+ cout << "\n" ;
+- cout << "\t\t\t\t\033[0;37;1;41m";
+- cout << " MUSTANG (v0.3): A MUltiple STuructural AligNment alGorithm. \033[0;0m\n" ;
++ cout << "\033[0;37;1;41m";
++ cout << " MUSTANG (v0.3): A MUltiple STructural AligNment alGorithm. \033[0;0m\n" ;
+ //cout << "\033[0;49m" ;
+- cout << "\t\t\t\t\033[1;33;4;1;46m";
++ cout << "\033[1;33;4;1;46m";
+ cout << "Authors: " ;
+ cout << "\033[0;1;37;4;1;46m" ;
+- cout << " A S Konagurthu, J Whisstock, and P J Stuckey, A M Lesk.\033[0m\n";
++ cout << " A S Konagurthu, J Whisstock, and P J Stuckey, A M Lesk. \033[0m\n";
+ //cout << "\033[0m" ;
+- cout << "\t\t\t\t\033[0;33;4;1;46m";
++ cout << "\033[0;33;4;1;46m";
+ cout << "(Mis)Coding: " ; cout << "\033[0;37;4;1;46m" ;
+- cout << " A S Konagurthu. \033[0m\n";
++ cout << " A S Konagurthu. \033[0m\n";
+ cout << "\033[0m" ;
+ cout << "\n\n" ;
+ }
Added: trunk/packages/mustang/trunk/debian/patches/test_zf-cchh.dpatch
===================================================================
--- trunk/packages/mustang/trunk/debian/patches/test_zf-cchh.dpatch (rev 0)
+++ trunk/packages/mustang/trunk/debian/patches/test_zf-cchh.dpatch 2008-01-10 15:46:49 UTC (rev 1094)
@@ -0,0 +1,50 @@
+#! /bin/sh /usr/share/dpatch/dpatch-run
+## test_zf_cchh by Morten Kjeldgaard <mok at bioxray.dk>
+##
+## DP: Fix the test command file so it makes use of the pdb entries
+## DP: that have been downloaded.
+
+ at DPATCH@
+diff -urNad mustang-3.0.orig~/data/test/test_zf-CCHH mustang-3.0.orig/data/test/test_zf-CCHH
+--- mustang-3.0.orig~/data/test/test_zf-CCHH 2007-08-18 02:39:49.000000000 +0200
++++ mustang-3.0.orig/data/test/test_zf-CCHH 2007-08-18 02:40:05.000000000 +0200
+@@ -17,26 +17,26 @@
+ ###############################################################################################
+
+
+- > ./data/test/pdbs
++ > /tmp
+
+-+1ard.pdb
+-+1bboN.pdb
+- + 1paa.pdb
++#+1ard.pdb
++#+1bboN.pdb
++# + 1paa.pdb
+ +1sp1.pdb
+ +1sp2.pdb
+
+- + 1zaa1.pdb
+-+1zaa2.pdb
+-+1zaa3.pdb
+-+1zfd.pdb
++# + 1zaa1.pdb
++#+1zaa2.pdb
++#+1zaa3.pdb
++#+1zfd.pdb
+
+
+-+1znf.pdb
+-+1znm.pdb
+-+2drp1.pdb
+-+2drp2.pdb
++#+1znf.pdb
++#+1znm.pdb
++#+2drp1.pdb
++#+2drp2.pdb
+ +3znf.pdb
+
+-+5znf.pdb
++#+5znf.pdb
+ #+test1.pdb
+ #+test2.pdb
Added: trunk/packages/mustang/trunk/debian/rules
===================================================================
--- trunk/packages/mustang/trunk/debian/rules (rev 0)
+++ trunk/packages/mustang/trunk/debian/rules 2008-01-10 15:46:49 UTC (rev 1094)
@@ -0,0 +1,76 @@
+#!/usr/bin/make -f
+# -*- mode: makefile; mode: font-lock -*-
+
+# Uncomment this to turn on verbose mode.
+#export DH_VERBOSE=1
+
+include /usr/share/dpatch/dpatch.make
+
+CFLAGS = -Wall -g
+
+ifneq (,$(findstring noopt,$(DEB_BUILD_OPTIONS)))
+ CFLAGS += -O0
+else
+ CFLAGS += -O2
+endif
+
+
+get-orig-source:
+ wget http://www.cs.mu.oz.au/~arun/mustang/mustang_v.3.tgz -O ../mustang_3.0.orig.tar.gz
+ gunzip ../mustang_3.0.orig.tar.gz
+ tar -f ../mustang_3.0.orig.tar --delete MUSTANG_v.3/data/test/pdbs/
+ gzip ../mustang_3.0.orig.tar
+
+build: build-stamp
+
+build-stamp: patch-stamp
+ dh_testdir
+
+ # Compile Mustang:
+ $(MAKE)
+ touch $@
+
+clean: unpatch
+ dh_testdir
+ dh_testroot
+ rm -f build-stamp
+
+ # Clean up after the build process.
+ rm -f obj/*.o
+ rm -f bin/MUSTANG_v.3
+ dh_clean
+
+install: build
+ dh_testdir
+ dh_testroot
+ dh_clean -k
+ dh_installdirs
+
+ #$(MAKE) DESTDIR=$(CURDIR)/debian/mustang install
+ install -D -m755 bin/MUSTANG_v.3 debian/mustang/usr/bin/mustang
+
+binary-indep:
+ # nothing to do here
+
+# Build architecture-dependent files here.
+binary-arch: build install
+ dh_testdir
+ dh_testroot
+ dh_installchangelogs
+ dh_installdocs
+ dh_installexamples data/test/* debian/runtest
+ dh_installman
+ dh_link
+ dh_strip
+ dh_compress
+ dh_fixperms
+ dh_installdeb
+ dh_shlibdeps
+ dh_gencontrol
+ dh_md5sums
+ dh_builddeb
+
+binary: binary-arch
+.PHONY: build clean binary-arch binary install
+
+####
Property changes on: trunk/packages/mustang/trunk/debian/rules
___________________________________________________________________
Name: svn:executable
+ *
Added: trunk/packages/mustang/trunk/debian/runtest
===================================================================
--- trunk/packages/mustang/trunk/debian/runtest (rev 0)
+++ trunk/packages/mustang/trunk/debian/runtest 2008-01-10 15:46:49 UTC (rev 1094)
@@ -0,0 +1,24 @@
+#!/bin/sh
+# pdbget script for mustang that fetches
+# db entries to run test file.
+#
+set -e
+
+SERVER=www.pdb.org
+entries="1sp1 1sp2 3znf"
+
+pdb_fetch () {
+ for n in $* ; do
+ wget -nv http://${SERVER}/pdb/files/$n.pdb.gz
+ done
+}
+
+savedir=$PWD
+cd /tmp
+pdb_fetch $entries
+for f in $entries; do gzip -dc $f.pdb.gz > $f.pdb ; done
+
+mustang -f /usr/share/doc/mustang/examples/test_zf-CCHH
+cd $savedir
+
+echo Results are in /tmp/results.html and /tmp/results.pdb
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