--- ball-1.3.2.orig/debian/README.source +++ ball-1.3.2/debian/README.source @@ -0,0 +1,7 @@ +The installation files for Windows and MacOS were not removed +from the source tree. This would have slightly reduced the +source code, but would have increased difficulties for remote +administrators to provide homogeneous distributed environments. +For scientific computing such reliability is essential. + + -- Steffen Moeller Tue, 21 Jul 2009 22:40:21 +0200 --- ball-1.3.2.orig/debian/python-ball.dirs +++ ball-1.3.2/debian/python-ball.dirs @@ -0,0 +1 @@ +usr/share/BALL --- ball-1.3.2.orig/debian/changelog +++ ball-1.3.2/debian/changelog @@ -0,0 +1,87 @@ +ball (1.3.2-2) unstable; urgency=low + + [Andreas Hildebrandt] + * Improvements for CMake build system (Closes: 546311) + * Some fixes for less common architectures and fixes in the sip dependencies + (Closes: 565694) + [Jonathan Wiltshire] + * Depend on python-support and call dh_pysupport in debian/rules. + Let python-support decide dependencies for python-ball and python-ballview. + (Closes: #566036) + + -- Andreas Hildebrandt Thu, 11 Feb 2010 22:15:09 +0100 + +ball (1.3.2-1) unstable; urgency=low + + * Updated to new upstream release 1.3.2 + + -- Andreas Hildebrandt Tue, 19 Jan 2010 12:34:33 +0100 + +ball (1.3.1-2) unstable; urgency=low + + * Add python-sip4 as an explicit build-dependency (fixes an FTBFS) + + -- Andreas Hildebrandt Tue, 12 Jan 2010 10:25:36 +0100 + +ball (1.3.1-1) unstable; urgency=low + + * Updated to new upstream release 1.3.1 (Closes: 551241) + * Switched from autoconf to CMake (Closes: 552809) + + -- Andreas Hildebrandt Fri, 18 Dec 2009 14:20:08 +0100 + +ball (1.3.0-2) UNRELEASED; urgency=low + + [ Andreas Hildebrandt ] + * Increased dependency to python-sip4 to version 4.8.2, which + would need to be adjusted for lenny (4.7.2). The real (unexpressable) + dependency is to have the same version at build- and run-time. [Steffen] + + [ Charles Plessy ] + * Documented informations in ‘debian/upstream-metadata.yaml’. + + -- Andreas Hildebrandt Thu, 17 Sep 2009 22:30:28 +0200 + +ball (1.3.0-1) unstable; urgency=low + + * New upstream release + * BALL no longer uses gSoap (Closes: #542215) + * Added s390 to list of supported processors (Closes: #546311) + * Fixed broken maintainer address (Closes: #544932) + * Updated policy-compliance to 3.8.3 (no changes reguired) + * Updated build-dependencies to demand more recent libtool + + -- Andreas Hildebrandt Thu, 17 Sep 2009 22:30:28 +0200 + +ball (1.3+rc2-1) unstable; urgency=low + + * Removed debian/copyright entries for files no longer in the repository + * Updated to new upstream release candidate + * Removed build-dependency on libboost-asio-dev (Closes: #542251) + * Some small packaging improvements + + -- Andreas Hildebrandt Thu, 17 Sep 2009 22:25:51 +0200 + +ball (1.3+beta2.1-2) unstable; urgency=low + + * Re-upload upon initial rejection to improve debian/copyright (Closes: #407665) + * Improved Doc-Base + * Eliminated two lintian warnings + + -- Andreas Hildebrandt Sun, 16 Aug 2009 01:23:30 +0200 + +ball (1.3+beta2.1-1) UNRELEASED; urgency=low + + * Preparing for new upstream version 1.3 (Closes: #407665) + * Improvements for Debian packaging + - providing VIEW-independent and -dependent debs + - corrected for problematic copyright statements + + -- Andreas Hildebrandt Mon, 6 Jul 2009 17:43:00 +0100 + +ball (1.2-1) UNRELEASED; urgency=low + + * Initial packaging + + -- Andreas Hildebrandt Sun, 16 Nov 2008 20:24:32 +0100 + --- ball-1.3.2.orig/debian/libball.dirs +++ ball-1.3.2/debian/libball.dirs @@ -0,0 +1,3 @@ +usr/lib +usr/share/BALL +usr/share/BALL/doc --- ball-1.3.2.orig/debian/ballview.lintian-overrides +++ ball-1.3.2/debian/ballview.lintian-overrides @@ -0,0 +1,2 @@ +ballview binary: postinst-does-not-call-installdocs +ballview binary: prerm-does-not-call-installdocs --- ball-1.3.2.orig/debian/BALLView +++ ball-1.3.2/debian/BALLView @@ -0,0 +1,7 @@ +#!/bin/sh +export LD_LIBRARY_PATH=/usr/lib/BALL +export BALL_DATA_PATH=/usr/share/BALL/data +export PYTHONPATH=/usr/lib/BALL/ +# set Antialiasing for NVIDIA cards +export __GL_FSAA_MODE=6 +/usr/lib/BALL/BALLView $@ --- ball-1.3.2.orig/debian/libball-dev.dirs +++ ball-1.3.2/debian/libball-dev.dirs @@ -0,0 +1,2 @@ +usr/include +usr/lib --- ball-1.3.2.orig/debian/libballview-dev.dirs +++ ball-1.3.2/debian/libballview-dev.dirs @@ -0,0 +1,2 @@ +usr/include +usr/lib --- ball-1.3.2.orig/debian/libball1.3-doc.doc-base.manual +++ ball-1.3.2/debian/libball1.3-doc.doc-base.manual @@ -0,0 +1,13 @@ +Document: ball-manual +Title: Developers' manual for BALL, the Biochmical Algorithms Library +Author: The developers of BALL +Abstract: BALL (Biochemical Algorithms Library) is an application framework + in C++ that has been specifically designed for rapid software + development in Molecular Modeling and Computational Molecular Biology. + The library documentation comprises an extensive manual on how to program molecular + modelling programs with BALL. +Section: Science/Chemistry + +Format: HTML +Index: /usr/share/doc/libball1.3/html/BALL/index.html +Files: /usr/share/doc/libball1.3/html/BALL/*.html --- ball-1.3.2.orig/debian/ballview.dirs +++ ball-1.3.2/debian/ballview.dirs @@ -0,0 +1,3 @@ +usr/bin +usr/share/man/man1 +usr/share/doc/ballview/html --- ball-1.3.2.orig/debian/createBALLDeb +++ ball-1.3.2/debian/createBALLDeb @@ -0,0 +1,116 @@ +#!/bin/bash -x +# script to create a Debian binary package while creating a source package + +# bail out when a command has a non-zero return value +set -e + +VERSION="1.3" +PREFIX=/usr +export BALL_PATH=`pwd | sed -e 's%/debian$%%' -e 's%/debian-upstream$%%'` +if [ ! -d "$BALL_PATH" ]; then + echo "$0: source root directory '$BALL_PATH' is not existing." + echo "Pwd: " `pwd` + exit -1 +fi +export BALL_INSTALL_PATH=${BALL_PATH}/build/${PREFIX}/ + +# we will need the python version used to build our modules later +PYTHON_VERSION=$(ldd ${BALL_INSTALL_PATH}/lib/BALLCore.so | grep python | sed "s_^.*libpython\(...\).*_\1_") + +# and the corresponding site-packages path (without the leading /usr) +PYTHON_SITE_PATH=$(python${PYTHON_VERSION} -c "import distutils.sysconfig; print distutils.sysconfig.get_python_lib(0,0)[4:];") + +cd $BALL_PATH/debian +mkdir -p libball${VERSION}${PREFIX}/lib \ + libball${VERSION}${PREFIX}/share/BALL \ + libball${VERSION}${PREFIX}/share/BALL/doc \ + libball${VERSION}-dev${PREFIX}/include \ + libball${VERSION}-dev${PREFIX}/lib \ + libballview${VERSION}${PREFIX}/lib \ + libballview${VERSION}-dev${PREFIX}/include/BALL \ + libballview${VERSION}-dev${PREFIX}/lib \ + libball${VERSION}-doc${PREFIX}/share/doc/libball${VERSION}/html \ + python-ball${PREFIX}/share/BALL \ + python-ball${PREFIX}/${PYTHON_SITE_PATH} \ + python-ballview${PREFIX}/${PYTHON_SITE_PATH} \ + ballview${PREFIX}/bin \ + ballview${PREFIX}/share/man/man1 \ + ballview${PREFIX}/share/doc/ballview/html \ + ballview${PREFIX}/share/applications \ + ballview${PREFIX}/share/pixmaps \ + ballview${PREFIX}/share/BALL/data/graphics + +# remember the targets of the ldconfig symbolic links +LIBBALL_TARGET=$(ls -l ${BALL_INSTALL_PATH}/lib/libBALL.so) +LIBBALL_TARGET=${LIBBALL_TARGET#* -> } +LIBBALL_TARGET=$(basename ${LIBBALL_TARGET}) + +LIBVIEW_TARGET=$(ls -l ${BALL_INSTALL_PATH}/lib/libVIEW.so) +LIBVIEW_TARGET=${LIBVIEW_TARGET#* -> } +LIBVIEW_TARGET=$(basename ${LIBVIEW_TARGET}) + +# get rid of the symbolic links before we copy anything +rm ${BALL_INSTALL_PATH}/lib/libBALL.so +rm ${BALL_INSTALL_PATH}/lib/libVIEW.so + +cp ${BALL_INSTALL_PATH}/lib/libBALL*.so.* libball${VERSION}${PREFIX}/lib/ +cp ${BALL_INSTALL_PATH}/lib/libVIEW*.so.* libballview${VERSION}${PREFIX}/lib/ +cp -r ${BALL_INSTALL_PATH}/share/BALL/data libball${VERSION}${PREFIX}/share/BALL +cp -r ${BALL_INSTALL_PATH}/include/BALL libball${VERSION}-dev${PREFIX}/include +cp -r ${BALL_INSTALL_PATH}/include/BALL/VIEW libballview${VERSION}-dev${PREFIX}/include/BALL +# CMake does not build .la files by default... +#cp ${BALL_INSTALL_PATH}/lib/libBALL.la libball${VERSION}-dev${PREFIX}/lib +#cp ${BALL_INSTALL_PATH}/lib/libVIEW.la libballview${VERSION}-dev${PREFIX}/lib + +# debian needs the logo in the ballview - package, not in the libball +cp libball${VERSION}${PREFIX}/share/BALL/data/graphics/ballview*.xpm ballview${PREFIX}/share/pixmaps/ + +# get rid of the VIEW includes in libball-dev +rm -rf libball${VERSION}-dev${PREFIX}/include/BALL/VIEW + +# FIXME: the links should be relative! Steffen +ln -s ${LIBBALL_TARGET} libball${VERSION}-dev${PREFIX}/lib/libBALL.so +ln -s ${LIBVIEW_TARGET} libballview${VERSION}-dev${PREFIX}/lib/libVIEW.so +cp ${BALL_INSTALL_PATH}/bin/BALLView ballview${PREFIX}/bin/ +cp ballview.desktop ballview${PREFIX}/share/applications/ + +# if you want static libs, uncomment the following two lines +#mv libball${VERSION}${PREFIX}/lib/libBALL.a libball${VERSION}-dev${PREFIX}/lib && +#mv libball${VERSION}${PREFIX}/lib/libVIEW.a libball${VERSION}-dev${PREFIX}/lib && + +# copy the documentation +cp -r ${BALL_INSTALL_PATH}/share/BALL/doc/BALLView/* ballview${PREFIX}/share/doc/ballview/html +cp ${BALL_INSTALL_PATH}/share/BALL/doc/TUTORIAL/tutorial.pdf libball${VERSION}-doc${PREFIX}/share/doc/libball${VERSION}/ +cp -r ${BALL_INSTALL_PATH}/share/BALL/doc/classes libball${VERSION}${PREFIX}/share/BALL/doc +cp -r ${BALL_INSTALL_PATH}/share/BALL/doc/internal libball${VERSION}${PREFIX}/share/BALL/doc +# we need the BALLView documentation in the data path as well... sorry for that +cp -r ${BALL_INSTALL_PATH}/share/BALL/doc/BALLView libball${VERSION}${PREFIX}/share/BALL/doc +cp -r ${BALL_INSTALL_PATH}/share/BALL/doc/BALL libball${VERSION}-doc${PREFIX}/share/doc/libball${VERSION}/html + +gzip -9 -c ${BALL_PATH}/debian/ballview.1 > ballview${PREFIX}/share/man/man1/ballview.1.gz +gzip -9 -c ${BALL_PATH}/debian/ballview.1 > ballview${PREFIX}/share/man/man1/BALLView.1.gz + +cp -r ${BALL_PATH}/source/EXAMPLES/PYTHON python-ball${PREFIX}/share/BALL +cp ${BALL_INSTALL_PATH}/lib/BALL.py python-ball${PREFIX}/${PYTHON_SITE_PATH} +cp ${BALL_INSTALL_PATH}/lib/BALLCore.so python-ball${PREFIX}/${PYTHON_SITE_PATH} +cp ${BALL_INSTALL_PATH}/lib/VIEW.so python-ballview${PREFIX}/${PYTHON_SITE_PATH} + +chmod ugo-x libball${VERSION}${PREFIX}/share/BALL/data/QSAR/* +chmod ugo-x libball${VERSION}${PREFIX}/share/BALL/data/CHARMM/charmm* +chmod ugo-x libball${VERSION}${PREFIX}/share/BALL/data/graphics/* +chmod ugo-x libball${VERSION}${PREFIX}/share/BALL/data/structures/* +chmod 755 libball${VERSION}${PREFIX}/share/BALL/data/structures/DB/ +chmod ugo+x ballview${PREFIX}/bin/BALLView +chmod ugo-x python-ball${PREFIX}/share/BALL/PYTHON/*.py + +# remove spurious rpaths +chrpath -d ballview${PREFIX}/bin/BALLView +chrpath -d python-ball${PREFIX}/${PYTHON_SITE_PATH}/*.so +chrpath -d python-ballview${PREFIX}/${PYTHON_SITE_PATH}/*.so + +strip --strip-unneeded libball${VERSION}${PREFIX}/lib/*.so* +strip --strip-unneeded libballview${VERSION}${PREFIX}/lib/*.so* +strip --strip-unneeded ballview${PREFIX}/bin/* +strip --strip-unneeded python-ball${PREFIX}/${PYTHON_SITE_PATH}/*.so* +strip --strip-unneeded python-ballview${PREFIX}/${PYTHON_SITE_PATH}/*.so* + --- ball-1.3.2.orig/debian/ballview.desktop +++ ball-1.3.2/debian/ballview.desktop @@ -0,0 +1,10 @@ +[Desktop Entry] +Version=1.0 +Terminal=false +Icon=ballview +Exec=BALLView +Name=BALLView +GenericName=Molecular modeling and visualization tool +Type=Application +MimeType=chemical/x-pdb;chemical/x-mdl-molfile;chemical/x-mol2; +Categories=Education;Science;Chemistry; --- ball-1.3.2.orig/debian/ballview.1 +++ ball-1.3.2/debian/ballview.1 @@ -0,0 +1,54 @@ +.\" Copyright 1998-2009 BALL project group +.TH BALLView 1 "24 January 2009" +.SH NAME +BALLView - A free molecular modeling and molecular graphics tool +.SH SYNOPSIS +.B BALLView +.RI [Molecular-file] +.SH DESCRIPTION +.B BALLView +BALLView provides fast OpenGL-based visualization of molecular structures, +molecular mechanics methods (minimization, MD simulation using the +AMBER and CHARMM force fields), calculation and visualization +of electrostatic properties (FDPB). +.P +BALLView is based on BALL (Biochemical Algorithms Library) , +which is currently being developed in the groups of Oliver Kohlbacher +(University of Tuebingen, Germany), Andreas Hildebrandt (Saarland +University, Saarbruecken, Germany), and Hans-Peter Lenhof (Saarland +University, Saarbruecken, Germany). BALL is an application framework +in C++ that has been specifically designed for rapid software +development in Molecular Modeling and Computational Molecular Biology. +It provides an extensive set of data structures as well as classes +for Molecular Mechanics, advanced solvation methods, comparison and +analysis of protein structures, file import/export, and visualization. +.P +BALLView is available under the LGPL licence. +.P +Homepage: www.BALLView.org +.SH USAGE +.PP +To run BALLView, simply type: +.PP +.RS +BALLView +.P +or +.P +BALLView file.pdp +.RE +.PP +where +.I file.pdb +is your PDB file. BALLView also supports HIN, MOL, MOL2 and SD files. +.P +BALLView provides HTML documentation, that is available in the application +itself (see Help menu). +.P +This package also includes Python example scripts, that can be run in BALLView. +They can be found under /usr/share/BALL/PYTHON. +.SH AUTHOR +BALLView is copyright 1998-2009 by the BALL project group +.SH "SEE ALSO" +.br +.B http://www.ballview.org --- ball-1.3.2.orig/debian/watch +++ ball-1.3.2/debian/watch @@ -0,0 +1,3 @@ +version=3 +opts=uversionmangle=s/-(.*)/+$1/ \ +http://ball-www.bioinf.uni-sb.de/Releases/all/BALL-(.*)\.tar\.gz --- ball-1.3.2.orig/debian/libball1.3-doc.lintian-overrides +++ ball-1.3.2/debian/libball1.3-doc.lintian-overrides @@ -0,0 +1,2 @@ +libball1.3-doc binary: postinst-does-not-call-installdocs +libball1.3-doc binary: prerm-does-not-call-installdocs --- ball-1.3.2.orig/debian/libballview.dirs +++ ball-1.3.2/debian/libballview.dirs @@ -0,0 +1 @@ +usr/lib --- ball-1.3.2.orig/debian/debian-ball-install +++ ball-1.3.2/debian/debian-ball-install @@ -0,0 +1,51 @@ +#!/bin/bash +# script to build BALL / BALLView to create and compile a Debian/Ubuntu source package + +set -e + +#adapt to your settings +export BALL_PATH=`pwd | sed -e 's%/debian-upstream$%%g' -e 's%/debian$%%g'` +if [ ! -d "$BALL_PATH" ]; then + echo "$0: cannot find directory '$BALL_PATH' as presumed root of the source tree." + echo "Pwd: " `pwd` + exit -1 +fi +unset QTDIR +echo $1 + +if [ "$1" == "configure" ] +then + cd $BALL_PATH + mkdir build && cd build && cmake .. -DCMAKE_INSTALL_PREFIX=./usr -DBALL_PATH=/usr + exit $? +fi + +if [ "$1" == "build" ] +then + cd $BALL_PATH/build && make -j 2 all doc doc_tutorial install +# cd $BALL_PATH/source && echo "Running doxygen... This can take a while..." && make doc && echo "Doxygen done!" && make depend && mymake && make install +# cd $BALL_PATH/source/PYTHON/EXTENSIONS && mymake && make install +# cd $BALL_PATH/source/APPLICATIONS/BALLVIEW && mymake + exit $? +fi + +if [ "$1" == "install" ] +then + bash debian/createBALLDeb source + exit $? +fi + +if [ "$1" == "clean" ] +then + cd $BALL_PATH/source + if [ -f Makefile ] + then + make clean + cd PYTHON/EXTENSIONS + make clean + rm -rf ../lib/Linux* + rm -rf ../doc/doxygen/latex/* + rm -f $BALL_PATH/source/config.status 2>/dev/null + fi + exit $? +fi --- ball-1.3.2.orig/debian/libball1.3-doc.doc-base.tutorial +++ ball-1.3.2/debian/libball1.3-doc.doc-base.tutorial @@ -0,0 +1,12 @@ +Document: ball-tutorial +Title: BALL Programming Tutorial +Author: Andreas Hildebrandt +Abstract: BALL (Biochemical Algorithms Library) is an application framework + in C++ that has been specifically designed for rapid software + development in Molecular Modeling and Computational Molecular Biology. + This tutorial contains a small structured introduction into programming + with BALL. +Section: Science/Chemistry + +Format: PDF +Files: /usr/share/doc/libball1.3/tutorial.pdf.gz --- ball-1.3.2.orig/debian/copyright +++ ball-1.3.2/debian/copyright @@ -0,0 +1,105 @@ +This package was debianized by Andreas Moll (2007) +and Andreas Hildebrandt (2008-2009), with some +assistance by Steffen Moeller and first completed +on Mon, 17 Aug 2009 16:49:06 +0200. + +It was downloaded from http://ball-www.bioinf.uni-sb.de/Releases/all/ + +Main Upstream Authors: + + Andreas Hildebrandt , + Oliver Kohlbacher , + Andreas Moll + + Further contributers as listed on http://www.ballview.org/Overview/Team : + + Tim Aubertin, Christian Bender, Andreas Bertsch, Nicolas Pascal + Boghossian, Andreas Burchardt, Andreas Crauser, Anna Dehof, Carla + Haid, Andreas Kerzmann, Heiko Klein, Hans-Peter Lenhof, Bettina + Leonhardt, Peter Müller, Stefan Strobel, Marc Sturm + + +Copyright: 1998-2009, the BALL project group + +License: + + This package is free software; you can redistribute it and/or + modify it either under the terms of the GNU Lesser General Public + License (libraries) or the GNU General Public License (the ballview + application) as published by the Free Software Foundation; either + version 2 of the License, or (at your option) any later version. + The respective source code will indicate which license is applying + for the code of your interest. If in doubt, contact the the authors. + + This package is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU + Lesser General Public License for more details. + + You should have received a copy of the GNU Lesser General Public + License along with this package; if not, write to the Free Software + Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA + +File: source/configure +Copyright: (C) 1992-6, 1998-2006 Free Software Foundation, Inc. +License: + This configure script is free software; the Free Software Foundation + gives unlimited permission to copy, distribute and modify it. + +File: source/config/m4/ltversion.m4 +Copyright: (C) 2004 Free Software Foundation, Inc. +Author: Scott James Remnant, 2004 +License: + This file is free software; the Free Software Foundation gives + unlimited permission to copy and/or distribute it, with or without + modifications, as long as this notice is preserved. + +File: source/config/m4/libtool.m4 +Copyright: (C) 1996-2008 Free Software Foundation, Inc. +Author: Gordon Matzigkeit, 1996 + + This file is part of GNU Libtool. + + GNU Libtool is free software; you can redistribute it and/or + modify it under the terms of the GNU General Public License as + published by the Free Software Foundation; either version 2 of + the License, or (at your option) any later version. + + As a special exception to the GNU General Public License, + if you distribute this file as part of a program or library that + is built using GNU Libtool, you may include this file under the + same distribution terms that you use for the rest of that program. + + GNU Libtool is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + GNU General Public License for more details. + + You should have received a copy of the GNU General Public License + along with GNU Libtool; see the file COPYING. If not, a copy + can be downloaded from http://www.gnu.org/licenses/gpl.html, or + obtained by writing to the Free Software Foundation, Inc., + 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA. + +File: source/config/m4/ax_boost_*.m4 +Copyright: (C) 2008 Thomas Porschberg , Michael Tindal, + Daniel Casimiro , +License: + Copying and distribution of this file, with or without modification, are + permitted in any medium without royalty provided the copyright notice + and this notice are preserved. + +File: source/config/m4/ac_python_devel.m4 +Copyright: (C) 2008 Sebastian Huber + Alan W. Irwin , Rafael Laboissiere + , Andrew Collier , + Matteo Settenvini , Horst Knorr +License: GPL3+ + +On Debian systems, the complete text of the GNU Lesser General Public +License can be found in `/usr/share/common-licenses/LGPL-2' and the GNU +Public License can be found in `/usr/share/common-licenses/GPL-2'. + +The Debian packaging is (C) 2007-8, Andreas Moll +and Andreas Hildebrandt and is licensed under +the GPL, see `/usr/share/common-licenses/GPL'. --- ball-1.3.2.orig/debian/upstream-metadata.yaml +++ ball-1.3.2/debian/upstream-metadata.yaml @@ -0,0 +1,21 @@ +# Collection of meta-data about the upstream project, +# see http://wiki.debian.org/UpstreamMetadata for reference. + +Contact: BALL authors +DOI: 10.1093/bioinformatics/bti818 +Homepage: http://www.ballview.org +Name: BALL +PMID: 16332707 +Reference: + author: Moll, Andreas and Hildebrandt, Andreas and Lenhof, Hans-Peter and Kohlbacher, Oliver + title: BALLView: a tool for research and education in molecular modeling + journal: Bioinformatics + volume: 22 + number: 3 + pages: 365-366 + year: 2006 + URL: http://bioinformatics.oxfordjournals.org/cgi/content/abstract/22/3/365 + eprint: http://bioinformatics.oxfordjournals.org/cgi/reprint/22/3/365.pdf +Watch: | + opts=uversionmangle=s/-(.*)/+$1/ \ + http://ball-www.bioinf.uni-sb.de/Releases/all/BALL-(.*)\.tar\.gz --- ball-1.3.2.orig/debian/rules +++ ball-1.3.2/debian/rules @@ -0,0 +1,73 @@ +#!/usr/bin/make -f +# -*- makefile -*- +# Uncomment this to turn on verbose mode. +export DH_VERBOSE=1 + +CFLAGS = -Wall -g + +ifneq (,$(findstring noopt,$(DEB_BUILD_OPTIONS))) + CFLAGS += -O0 +else + CFLAGS += -O2 +endif + +configure: configure-stamp +configure-stamp: + dh_testdir + bash debian/debian-ball-install configure + touch $@ + +build: build-stamp +build-stamp: configure-stamp + dh_testdir + bash debian/debian-ball-install build + touch $@ + +clean: + dh_testdir + dh_testroot + bash debian/debian-ball-install clean + dh_clean build-stamp configure-stamp + +install: build + dh_testdir + dh_testroot + dh_clean -k + dh_installdirs + #DESTDIR=$(CURDIR)/debian/ballview + bash debian/debian-ball-install install + dh_pysupport + + +binary-indep: build install +binary-arch: build install + dh_testdir + dh_testroot + dh_installchangelogs + dh_installdocs + dh_installexamples +# dh_install + dh_installmenu +# dh_desktop +# dh_python + dh_installman -p ballview + dh_link + dh_strip -p libball1.3 + dh_compress + dh_fixperms + dh_makeshlibs + dh_installdeb + dh_shlibdeps + dh_gencontrol + dh_md5sums + dh_builddeb + +get-orig-source: + if [ -x /usr/bin/uscan ]; then \ + uscan --verbose --force-download ; \ + else \ + echo "uscan is not installed to perform the download." ; \ + fi + +binary: binary-indep binary-arch +.PHONY: build clean binary-indep binary-arch binary install configure --- ball-1.3.2.orig/debian/compat +++ ball-1.3.2/debian/compat @@ -0,0 +1 @@ +5 --- ball-1.3.2.orig/debian/README.Debian +++ ball-1.3.2/debian/README.Debian @@ -0,0 +1,22 @@ +The BALL suite for structural biology has an enormous flexibility in +its field of applications. There are so many, that a single group, +or even collaborating groups like the ones behind BALL, cannot provide +all the possible tools that would come handy to prepare the input for +BALL or to further interpret its output. The Debian community provides a +nice environment, very useful already, and we are happy to have further +contributed to it. + +The maintainer of this package is from BALL's upstream +development team (http://www.ballview.org). The Debian-Med community +(http://debian-med.alioth.debian.org) jumps in to lower the entry barriers +a bit. We all are very open towards new experiences and ideas about what +the distribution of BALL with Debian/Ubuntu might bring or has brought +for structural bioinformatics. If there are workflows (interactions +with other tools in Debian-Med) you are now experimenting with that +were previously too tedious to prepare or an increased accessibility of +distributed computing (clusters, clouds, ...?) then please drop us a note. + +Andreas Hildebrandt (on behalf of the BALL developers) and +Steffen Moeller (on behalf of Debian-Med) + + Tue, 21 Jul 2009 23:38:45 +0200 --- ball-1.3.2.orig/debian/ballview.menu +++ ball-1.3.2/debian/ballview.menu @@ -0,0 +1,7 @@ +?package(ballview):\ + needs="X11"\ + section="Applications/Science/Chemistry"\ + title="BALLView"\ + command="/usr/bin/BALLView"\ + icon="ballview_32x32.xpm"\ + longtitle="BALLView: A Molecular modeling and molecular graphics tool" --- ball-1.3.2.orig/debian/ballview.doc-base +++ ball-1.3.2/debian/ballview.doc-base @@ -0,0 +1,15 @@ +Document: ballview +Title: The ballview application's manual +Author: Andreas Hildebrandt +Abstract: BALLView is a free molecular modeling and molecular graphics tool + BALLView provides fast OpenGL-based visualization of molecular structures, + molecular mechanics methods (minimization, MD simulation using the + AMBER, CHARMM, and MMFF94 force fields), calculation and visualization + of electrostatic properties (FDPB) and molecular editing features. + The application's documentation is available as HTML and can be read + from within the program itself. +Section: Science/Chemistry + +Format: HTML +Index: /usr/share/doc/ballview/html/index.html +Files: /usr/share/doc/ballview/html/*.html --- ball-1.3.2.orig/debian/control +++ ball-1.3.2/debian/control @@ -0,0 +1,137 @@ +Source: ball +Section: science +Priority: optional +Maintainer: Andreas Hildebrandt +DM-Upload-Allowed: yes +Build-Depends: debhelper (>= 5), libqt4-dev, libqt4-gui, libqt4-opengl, + libqt4-opengl-dev, libqt4-sql, libqt4-network, sip4, python-sip4, + python-sip4-dev (>= 4.8.2), flex, bison, cmake, libglew1.5-dev|libglew-dev, + libfftw3-dev, libgsl0-dev, python-dev (>= 2.4), libxrender-dev, + libboost-dev, libboost-iostreams-dev, libboost-thread-dev, + libboost-math-dev | libboost-dev (<< 1.37), libboost-system-dev | libboost-dev (<< 1.37), + libasio-dev, libboost-regex-dev, libxmu-dev, doxygen, tidy, + texlive-base, texlive-latex-recommended, texlive-fonts-recommended, gs-common, + texlive-latex-extra, graphviz, chrpath, python-support (>= 0.90.0) +XS-Python-Version: all +Standards-Version: 3.8.3 +Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/ball/trunk/?rev=0&sc=0 +Vcs-Svn: svn://svn.debian.org/svn/debian-med/trunk/packages/ball/trunk/ +Homepage: http://www.ballview.org + +Package: libball1.3 +Section: science +Architecture: any +Depends: ${shlibs:Depends} ${misc:Depends} +Description: Biochemical Algorithms Library + BALL (Biochemical Algorithms Library) is an application framework + in C++ that has been specifically designed for rapid software + development in Molecular Modeling and Computational Molecular Biology. + It provides an extensive set of data structures as well as classes + for Molecular Mechanics, advanced solvation methods, comparison and + analysis of protein structures, file import/export, and visualization. + BALL is currently being developed in the groups of Oliver Kohlbacher + (University of Tuebingen, Germany), Andreas Hildebrandt (Saarland + University, Saarbruecken, Germany), and Hans-Peter Lenhof (Saarland + University, Saarbruecken, Germany). + . + This package contains the view - independent parts of BALL (libBALL, + data directories et al., except for libVIEW) and can be installed on + machines without X11. + +Package: libball1.3-dev +Section: libdevel +Architecture: any +Depends: libball1.3 (= ${binary:Version}) ${misc:Depends} +Recommends: libball1.3-doc +Description: Header files for the Biochemical Algorithms Library + This package comprises the header files allowing to create + one's own applications with the BALL library. + +Package: libballview1.3 +Section: science +Architecture: any +Depends: ${shlibs:Depends} ${misc:Depends} +Description: Biochemical Algorithms Library, VIEW framework + BALL (Biochemical Algorithms Library) is an application framework + in C++ that has been specifically designed for rapid software + development in Molecular Modeling and Computational Molecular Biology. + It provides an extensive set of data structures as well as classes + for Molecular Mechanics, advanced solvation methods, comparison and + analysis of protein structures, file import/export, and visualization. + BALL is currently being developed in the groups of Oliver Kohlbacher + (University of Tuebingen, Germany), Andreas Hildebrandt (Saarland + University, Saarbruecken, Germany), and Hans-Peter Lenhof (Saarland + University, Saarbruecken, Germany). + . + This package contains the view parts of BALL (libVIEW) required for + molecular visualization and required for running BALLView. + +Package: libballview1.3-dev +Section: libdevel +Architecture: any +Depends: libballview1.3 (= ${binary:Version}) ${misc:Depends} +Recommends: libball1.3-doc +Description: Header files for the VIEW part of the Biochemical Algorithms Library + BALL (Biochemical Algorithms Library) is an application framework + in C++ that has been specifically designed for rapid software + development in Molecular Modeling and Computational Molecular Biology. + This package comprises the header files allowing to create one's own + applications with the VIEW framework of the BALL library. + +Package: python-ball +Architecture: any +Section: python +Depends: ${shlibs:Depends}, ${python:Depends}, python-sip4 (>= 4.8.2), + libball1.3 ${misc:Depends} +Description: Python bindings for the Biochemical Algorithms Library + BALL (Biochemical Algorithms Library) is an application framework + in C++ that has been specifically designed for rapid software + development in Molecular Modeling and Computational Molecular Biology. + This package provides scripting access to the VIEW-independent functionality + of the Biochemical Algorithms Library (BALL). + +Package: python-ballview +Architecture: any +Section: python +Depends: ${shlibs:Depends}, ${python:Depends}, python-sip4 (>= 4.8.2), + libball1.3, libballview1.3 ${misc:Depends} +Description: Python bindings for VIEW-parts of the Biochemical Algorithms Library + BALL (Biochemical Algorithms Library) is an application framework + in C++ that has been specifically designed for rapid software + development in Molecular Modeling and Computational Molecular Biology. + This package provides scripting access to the VIEW-dependent functionality + of the Biochemical Algorithms Library (BALL). + +Package: ballview +Section: science +Architecture: any +Depends: ${shlibs:Depends}, libball1.3, libballview1.3, python-ball, + python-ballview ${misc:Depends} +Description: A free molecular modeling and molecular graphics tool + BALLView provides fast OpenGL-based visualization of molecular structures, + molecular mechanics methods (minimization, MD simulation using the + AMBER, CHARMM, and MMFF94 force fields), calculation and visualization + of electrostatic properties (FDPB) and molecular editing features. + . + BALLView can be considered a graphical user interface on the basis of + BALL (Biochemical Algorithms Library), having taken the most common + demands of protein chemists and biophysicists in particular taken into account. + which is currently being developed in the groups of Hans-Peter Lenhof + (Saarland University, Saarbruecken, Germany) and Oliver Kohlbacher + (University of Tuebingen, Germany). BALL is an application framework + in C++ that has been specifically designed for rapid software + development in Molecular Modeling and Computational Molecular Biology. + It provides an extensive set of data structures as well as classes + for Molecular Mechanics, advanced solvation methods, comparison and + analysis of protein structures, file import/export, and visualization. + +Package: libball1.3-doc +Architecture: all +Section: doc +Depends: libball1.3 ${misc:Depends} +Description: Documentation for the BALL library + BALL (Biochemical Algorithms Library) is an application framework + in C++ that has been specifically designed for rapid software + development in Molecular Modeling and Computational Molecular Biology. + The package comprises an extensive manual on how to program molecular + modelling programs with BALL.