New packging and bundling scripts

deployment/linux/README.txt

@@ -4,13 +4,3 @@ HOW TO USE THE BUNDLE SCRIPTS:
 2. Move to the <OpenStructure folder>/deployment/linux folder and start the create_bundle.py script using python
 3. In <OpenStructure> you'll find a tar.gz file. That's the bundle!
 4. If the process stops without completing, run the reset_repository.py script or delete the <OpenStructure Folder> and restart from scratch
-
-
-HOW TO USE THE QMEAN BUNDLE SCRIPTS:
-
-1. Checkout a copy of the OpenStructure repository.
-2. Check out a copy of the scratch repository in modules/scratch
-3. Create a folder called ChemLib in the <OpenStructure Folder> and copy the compunds.chemlib file into it.
-4. Move to the <OpenStructure folder>/deployment/linux folder and start the create_qmeqn_bundle.py script using python
-3. In <OpenStructure> you'll find a tar.gz file. That's the bundle!
-4. If the process stops without completing, run the reset_qmean_repository.py script or delete the <OpenStructure Folder> and restart from scratch
\ No newline at end of file

deployment/linux/create_bundle.py

@@ -12,7 +12,7 @@ if len(sys.argv) < 3:
   print 'usage: create_bundle.py  additional_label system_python_version'
   sys.exit()
 
-system_python_version=sys.argv[2]
+system_python_version='python'+sys.argv[2]
 system_python_bin='/usr/bin/'+system_python_version
 system_python_libs='/usr/lib/'+system_python_version
 second_system_python_libs_flag=True
@@ -43,28 +43,21 @@ date_pattern='%Y-%b-%d'
 build=datetime.date.today()
 directory_name='openstructure-linux-'+archstring+'-'+additional_label+'-'+str(build)
 print 'Hardcoding package python binary path in openstructure executables'
-subprocess.call('mv scripts/ost.in scripts/ost.in.backup',shell=True,cwd='../../')
-subprocess.call('sed "s/@PYTHON_BINARY@/\$DNG_ROOT\/bin\/'+python_bin_in_bundle+'/g" scripts/ost.in.backup > scripts/ost.in.prepreprepre',shell=True,cwd='../../')
-subprocess.call('sed "s/\#export LD_LIBRARY_PATH/ export LD_LIBRARY_PATH/g" scripts/ost.in.prepreprepre > scripts/ost.in.preprepre',shell=True,cwd='../../')
-subprocess.call('sed "s/\#export PYTHONHOME/ export PYTHONHOME/g" scripts/ost.in.preprepre > scripts/ost.in.prepre',shell=True,cwd='../../')
-subprocess.call('sed "s/\#export PYTHONPATH/ export PYTHONPATH/g" scripts/ost.in.prepre > scripts/ost.in.pre',shell=True,cwd='../../')
-subprocess.call('sed "s/\#export QT_PLUGIN_PATH/ export QT_PLUGIN_PATH/g" scripts/ost.in.pre > scripts/ost.in',shell=True,cwd='../../')
-subprocess.call('mv scripts/dng.in scripts/dng.in.backup',shell=True,cwd='../../')
-subprocess.call('sed "s/\#export LD_LIBRARY_PATH/ export LD_LIBRARY_PATH/g" scripts/dng.in.backup > scripts/dng.in.preprepre',shell=True,cwd='../../')
-subprocess.call('sed "s/\#export PYTHONHOME/ export PYTHONHOME/g" scripts/dng.in.preprepre > scripts/dng.in.prepre',shell=True,cwd='../../')
-subprocess.call('sed "s/\#export PYTHONPATH/ export PYTHONPATH/g" scripts/dng.in.prepre > scripts/dng.in.pre',shell=True,cwd='../../')
-subprocess.call('sed "s/\#export QT_PLUGIN_PATH/ export QT_PLUGIN_PATH/g" scripts/dng.in.pre > scripts/dng.in',shell=True,cwd='../../')
+subprocess.call('mv scripts/ost_config.in scripts/ost_config.in.backup',shell=True,cwd='../../')
+subprocess.call('sed "s/@PYTHON_BINARY@/\$DNG_ROOT\/bin\/'+python_bin_in_bundle+'/g" scripts/ost_config.in.backup > scripts/ost_config.in.preprepre',shell=True,cwd='../../')
+subprocess.call('sed "s/\#export PYTHONHOME/ export PYTHONHOME/g" scripts/ost_config.in.preprepre > scripts/ost_config.in.prepre',shell=True,cwd='../../')
+subprocess.call('sed "s/\#export PYTHONPATH/ export PYTHONPATH/g" scripts/ost_config.in.prepre > scripts/ost_config.in.pre',shell=True,cwd='../../')
+subprocess.call('sed "s/\#export QT_PLUGIN_PATH/ export QT_PLUGIN_PATH/g" scripts/ost_config.in.pre > scripts/ost_config.in',shell=True,cwd='../../')
 #print 'Downloading Chemlib dictionary'
 #subprocess.call('wget ftp://ftp.wwpdb.org/pub/pdb/data/monomers/components.cif', shell=True, cwd='../../')
 #print 'Compiling Openstructure'
 #subprocess.call('cmake ./ -DCMAKE_BUILD_TYPE=Release -DPREFIX='+directory_name+' -DBoost_COMPILER='+boost_string+'-DENABLE_IMG=OFF -DENABLE_UI=OFF -DENABLE_GFX=OFF', shell=True,cwd='../../')
 #subprocess.call('cmake ./ -DCMAKE_BUILD_TYPE=Release -DPREFIX='+directory_name+' s-DENABLE_IMG=OFF -DENABLE_UI=OFF -DENABLE_GFX=OFF', shell=True,cwd='../../')
 #subprocess.call('make -j5',shell=True,cwd='../../')
-#print 'Converting Chemlib dictionary'
-#subprocess.call('stage/bin/chemdict_tool create components.cif compounds.chemlib', shell=True, cwd='../../')
-#print '\nStaging Chemlib dictionary'
+##print 'Converting Chemlib dictionary'
+##subprocess.call('stage/bin/chemdict_tool create components.cif compounds.chemlib', shell=True, cwd='../../')
+print '\nStaging Chemlib dictionary'
 print 'Compiling Openstructure'
-#subprocess.call('cmake ./ -DCMAKE_BUILD_TYPE=Release -DPREFIX='+directory_name+' -DBoost_COMPILER='+boost_string+' -DCOMPOUND_LIB=ChemLib/compounds.chemlib -DENABLE_IMG=ON -DENABLE_UI=ON -DENABLE_GFX=ON -DOPTIMIZE=ON',shell=True,cwd='../../')
 subprocess.call('cmake ./ -DCMAKE_BUILD_TYPE=Release -DPREFIX='+directory_name+' -DCOMPOUND_LIB=ChemLib/compounds.chemlib -DENABLE_IMG=ON -DENABLE_UI=ON -DENABLE_GFX=ON -DOPTIMIZE=ON',shell=True,cwd='../../')
 subprocess.call('make -j2',shell=True,cwd='../../')
 print 'Removing obsolete packages and package directory'
@@ -73,13 +66,14 @@ print 'Creating new package directory'
 subprocess.call('mkdir '+directory_name,shell=True,cwd='../../')
 subprocess.call('mkdir '+directory_name+'/bin',shell=True,cwd='../../')
 print 'Copy python executable into stage for dependency detection'
+print system_python_bin
 subprocess.call('cp '+system_python_bin+ ' stage/bin/python',shell=True,cwd='../../')
 print 'Copy python libraries into the stage for dependency detection'
-subprocess.call('cp -pRL '+system_python_libs+' stage/'+libdir,shell=True,cwd='../../')
-subprocess.call('rm -fr stage/'+libdir+'/'+system_python_version+'/dist-packages',shell=True,cwd='../../')
+subprocess.call('cp -pRL '+system_python_libs+' stage/'+libdir+'/python',shell=True,cwd='../../')
+subprocess.call('rm -fr stage/'+libdir+'/python/dist-packages',shell=True,cwd='../../')
 if second_system_python_libs_flag==True:
-  subprocess.call('cp -pRL '+second_system_python_libs+'/sip* stage/'+libdir+'/'+system_python_version,shell=True,cwd='../../')
-  subprocess.call('cp -pRL '+second_system_python_libs+'/PyQt* stage/'+libdir+'/'+system_python_version,shell=True,cwd='../../')
+  subprocess.call('cp -pRL '+second_system_python_libs+'/sip* stage/'+libdir+'/python/',shell=True,cwd='../../')
+  subprocess.call('cp -pRL '+second_system_python_libs+'/PyQt* stage/'+libdir+'/python/',shell=True,cwd='../../')
 print 'Creating new dependency list'
 so_list=[]
 walk_list=os.walk('../../stage')
@@ -104,22 +98,21 @@ for entry in sorted_dep_list:
        exclude=True
    if exclude==False: 
      filtered_dep_list.append(entry)
+print 'Installing OpenStructure into package directory structure'
+subprocess.call('make install',shell=True,cwd='../../')
 print 'Copy libraries in the package directory structure'
-subprocess.call('mkdir '+directory_name+'/'+libdir,shell=True,cwd='../../')
 for entry in filtered_dep_list:
   subprocess.call('cp '+entry+' '+directory_name+'/'+libdir,shell=True,cwd='../../')
 print 'Copy python executable into package directory structure'
 subprocess.call('cp '+system_python_bin+ ' '+directory_name+'/bin/python',shell=True,cwd='../../')
 print 'Copy python libraries into package directory structure'
-subprocess.call('cp -pRL '+system_python_libs+' '+directory_name+'/'+libdir,shell=True,cwd='../../')
-subprocess.call('rm -fr '+directory_name+'/'+libdir+'/'+system_python_version+'/dist-packages',shell=True,cwd='../../')
+subprocess.call('cp -pRL '+system_python_libs+' '+directory_name+'/'+libdir+'/python',shell=True,cwd='../../')
+subprocess.call('rm -fr '+directory_name+'/'+libdir+'/python/dist-packages',shell=True,cwd='../../')
 if second_system_python_libs_flag==True:
-  subprocess.call('cp -pRL '+second_system_python_libs+'/sip* '+directory_name+'/'+libdir+'/'+system_python_version,shell=True,cwd='../../')
-  subprocess.call('cp -pRL '+second_system_python_libs+'/PyQt* '+directory_name+'/'+libdir+'/'+system_python_version,shell=True,cwd='../../')
+  subprocess.call('cp -pRL '+second_system_python_libs+'/sip* '+directory_name+'/'+libdir+'/python/',shell=True,cwd='../../')
+  subprocess.call('cp -pRL '+second_system_python_libs+'/PyQt* '+directory_name+'/'+libdir+'/python/',shell=True,cwd='../../')
 print 'Copy Qt 4 plugins into package directory structure'
 subprocess.call('cp -pRL '+qt4_plugins+' '+directory_name+'/bin/',shell=True,cwd='../../')
-print 'Installing OpenStructure into package directory structure'
-subprocess.call('make install',shell=True,cwd='../../')
 print 'Copying supplementary material into package directory structure'
 subprocess.call('cp -pRL  stage/share/openstructure  '+directory_name+'/share/',shell=True,cwd='../../')
 print 'Copying examples into package directory structure'
@@ -140,11 +133,8 @@ print 'removing dokk and harmony examples from bundle'
 subprocess.call('rm -rf '+directory_name+'/share/openstructure/examples/code_fragments/dokk',shell=True,cwd='../../')
 subprocess.call('rm -rf '+directory_name+'/share/openstructure/examples/code_fragments/harmony',shell=True,cwd='../../')
 print 'De-hardcoding package python binary path from openstructure executables'
-subprocess.call('rm scripts/ost.in',shell=True,cwd='../../')
-subprocess.call('rm scripts/ost.in.pre*',shell=True,cwd='../../')
-subprocess.call('rm scripts/dng.in',shell=True,cwd='../../')
-subprocess.call('rm scripts/dng.in.pre*',shell=True,cwd='../../')
-subprocess.call('mv scripts/ost.in.backup scripts/ost.in',shell=True,cwd='../../')
-subprocess.call('mv scripts/dng.in.backup scripts/dng.in',shell=True,cwd='../../')
+subprocess.call('rm scripts/ost_config.in',shell=True,cwd='../../')
+subprocess.call('rm scripts/ost_config.in.pre*',shell=True,cwd='../../')
+subprocess.call('mv scripts/ost_config.in.backup scripts/ost_config.in',shell=True,cwd='../../')
 subprocess.call('tar cfz '+directory_name+'.tgz '+directory_name,shell=True,cwd='../../')
 

deployment/linux/debian/README

+1. Checkout OpenStructure into a directory called strictly:'openstructure-<version>' (currently is 1.1d - 1.1 develop)
+2. Remove all the .git* files and directories from the source
+3. Create a compressed file with the source directory called strictly 'openstructure_<version>.orig.tar.gz' 
+   (At the same level as the source directory)
+4. Copy the 'debian' directory into the top level of the source directory
+5. Go into the top level of the source directory
+6. Build package with 'debuilder -uc -us'
+7. You can find the built package at the same level as the source directory and the source zipped file

deployment/linux/debian/debian/README.source

+===============OPENSTRUCTURE molecular modelling framework ===============
+
+
+OpenStructure is the next generation molecular modelling tailored at anybody
+ using 3D Structures or electron density maps.
+
+Please refer to www.openstructure.org for more information or try out
+ directly one of the binary packages available for download.
+
+Thank you for you interest and enjoy the straightforward way of handling 
+protein structure data!
+
+Please do not hesitate to contact us for feedback or troubleshooting:
+
+ost-users@maillist.unibas.ch 
+
+
+=============== The OpenStructure Team ===================================

deployment/linux/debian/debian/changelog

+openstructure (1.1d-0ubuntu1) natty; urgency=low
+
+  * Initial release 
+
+ -- Valerio Mariani <valerio.mariani@unibas.ch>  Wed, 13 Jul 2011 15:41:35 +0200

deployment/linux/debian/debian/chemdict_tool.1

+.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.38.4.
+.TH CHEMDICT_TOOL: "1" "July 2011" "User Commands"
+.SH NAME
+chemdict_tool \- compound libary creation tool for OpenStructure
+.SH SYNOPSIS
+chemdict_tool action <compound\-dict> <db> (pdb|charmm|amber|opls)
+.SH OPTIONS
+Supported actions are:
+.TP
+create
+\- creates a new db
+.TP
+update
+\- update existing db
+.SS "supported actions are:"
+.TP
+create
+\- creates a new db
+.TP
+update
+\- update existing db
+.SH "SEE ALSO"
+The full documentation for
+.B usage:
+is maintained as a Texinfo manual.  If the
+.B info
+and
+.B usage:
+programs are properly installed at your site, the command
+.IP
+.B info usage:
+.PP
+should give you access to the complete manual.

deployment/linux/debian/debian/compat

+7

deployment/linux/debian/debian/control

+Source: openstructure
+Section: science
+Priority: extra
+Maintainer: Valerio Mariani <valerio.mariani@unibas.ch>
+Build-Depends: debhelper (>= 7.0.50~),cmake,desktop-file-utils,libboost-all-dev,libeigen2-dev,qt4-dev-tools,libqt4-dev,libqt4-opengl-dev,python-qt4-dev,pyqt4-dev-tools,libfftw3-dev,libpng12-dev,libtiff4-dev,python-dev
+Standards-Version: 3.9.1
+Homepage: http://www.openstructure.org
+          
+Package: openstructure
+Architecture: any
+Depends: ${shlibs:Depends}, ${misc:Depends}, python-sip, python-qt4
+Description: Open-source computational structural biology framework
+ The Openstructure  project aims to provide an open-source, modular, flexible, 
+ molecular modelling and visualization environment. It is targeted at 
+ interested method developers in the field of structural bioinformatics.
+
+Package: openstructure-dev
+Architecture: any
+Depends: ${shlibs:Depends}, ${misc:Depends}, openstructure
+Description: Open-source computational structural biology framework
+ The Openstructure  project aims to provide an open-source, modular, flexible, 
+ molecular modelling and visualization environment. It is targeted at 
+ interested method developers in the field of structural bioinformatics.

deployment/linux/debian/debian/copyright

+Format: http://dep.debian.net/deps/dep5
+Upstream-Name: openstructure
+Source: http://www.openstructure.org
+
+Files: *
+Copyright: 2008-2011 Torsten Schwede <torsten.schwede@unibas.ch>
+License: LGPL-3.0
+
+Files: debian/*
+Copyright: 2011 Valerio Mariani <valerio.mariani@unibas.ch>
+License: LGPL-3.0
+
+License: LGPL-3.0
+ This package is free software; you can redistribute it and/or
+ modify it under the terms of the GNU Lesser General Public
+ License as published by the Free Software Foundation; either
+ version 3 of the License, or (at your option) any later version.
+ .
+ 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 General Public License
+ along with this program. If not, see <http://www.gnu.org/licenses/>.
+ .
+ On Debian systems, the complete text of the GNU Lesser General
+ Public License can be found in "/usr/share/common-licenses/LGPL-3".
+
+Files: modules/db/src/sqlite3.h, modules/db/src/sqlite.c
+Copyright: 2011 Valerio Mariani <valerio.mariani@unibas.ch>
+License: None
+ 2001 September 15
+ .
+ The author disclaims copyright to this source code.  In place of
+ a legal notice, here is a blessing:
+ .
+    May you do good and not evil.
+    May you find forgiveness for yourself and forgive others.
+    May you share freely, never taking more than you give.

deployment/linux/debian/debian/dng.1

+.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.38.4.
+.TH DNG "1" "July 2011" "User Commands"
+.SH NAME
+dng \- GUI for OpenStructure
+.SH SYNOPSIS
+.B dng
+[\fIoptions\fR] [\fIfiles to load\fR]
+.SH OPTIONS
+.TP
+\fB\-h\fR, \fB\-\-help\fR
+show this help message and exit
+.TP
+\fB\-v\fR VLEVEL, \fB\-\-verbosity_level\fR=\fIVLEVEL\fR
+sets the verbosity level [default: 2]
+.TP
+\fB\-s\fR SCRIPT, \fB\-\-script\fR=\fISCRIPT\fR
+executes a script (syntax: \fB\-s\fR SCRIPT [options] [args])
+Anything that follows this option is passed to the
+script
+.TP
+\fB\-p\fR PDB_IDS, \fB\-\-pdb_id\fR=\fIPDB_IDS\fR
+PDB file ID. The file will be retrieved from PDB
+.TP
+\fB\-b\fR BUILDER, \fB\-\-builder\fR=\fIBUILDER\fR
+Type of builder used by the progam (either RULE_BASED
+or HEURISTIC) [default: HEURISTIC]
+.TP
+\fB\-c\fR COMPLIB, \fB\-\-compound_library\fR=\fICOMPLIB\fR
+Compound library for the RULE_BASED builder (only used
+if \fB\-\-builder\fR option is set to RULE_BASED, otherwise
+ignored [default: compounds.chemlib]
+.TP
+\fB\-q\fR QUERY, \fB\-\-query\fR=\fIQUERY\fR
+Selection query to be highlighted automatically upon
+loading (only used together with \fB\-p\fR option or when a
+PDB file is loaded, otherwise ignored [default: None]
+.TP
+\fB\-S\fR, \fB\-\-stereo\fR
+try to get a quad\-buffer stereo visual

deployment/linux/debian/debian/openstructure.desktop

+[Desktop Entry]
+Name=OpenStructure
+GenericName=Open-Source Computational Structural Biology Framework
+Exec=dng
+Icon=openstructure
+Terminal=false
+Type=Application
+Categories=Education;Science;

deployment/linux/debian/debian/openstructure.manpages

+debian/ost.1
+debian/dng.1
+debian/chemdict_tool.1

deployment/linux/debian/debian/ost.1

+.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.38.4.
+.TH OST "1" "July 2011" "User Commands"
+.SH NAME
+ost: \- command-line console for OpenStructure
+.SH SYNOPSIS
+.B ost
+[\fIost options\fR] [\fIscript to execute\fR] [\fIscript parameters\fR]
+.SH OPTIONS
+.TP
+\fB\-i\fR, \fB\-\-interactive\fR
+start interpreter interactively (must be first
+parameter, ignored otherwise)
+.TP
+\fB\-h\fR, \fB\-\-help\fR
+show this help message and exit
+.TP
+\fB\-v\fR VLEVEL, \fB\-\-verbosity_level\fR=\fIVLEVEL\fR
+sets the verbosity level [default: 2]

deployment/linux/debian/debian/postinst

+#!/bin/sh
+# postinst script for openstructure
+#
+# see: dh_installdeb(1)
+
+set -e
+
+# summary of how this script can be called:
+#        * <postinst> `configure' <most-recently-configured-version>
+#        * <old-postinst> `abort-upgrade' <new version>
+#        * <conflictor's-postinst> `abort-remove' `in-favour' <package>
+#          <new-version>
+#        * <postinst> `abort-remove'
+#        * <deconfigured's-postinst> `abort-deconfigure' `in-favour'
+#          <failed-install-package> <version> `removing'
+#          <conflicting-package> <version>
+# for details, see http://www.debian.org/doc/debian-policy/ or
+# the debian-policy package
+
+
+case "$1" in
+    configure)
+    ldconfig
+    ;;
+
+    abort-upgrade|abort-remove|abort-deconfigure)
+    ;;
+
+    *)
+        echo "postinst called with unknown argument \`$1'" >&2
+        exit 1
+    ;;
+esac
+
+# dh_installdeb will replace this with shell code automatically
+# generated by other debhelper scripts.
+
+#DEBHELPER#
+
+exit 0

deployment/linux/debian/debian/rules

+#!/usr/bin/make -f
+# -*- makefile -*-
+# Sample debian/rules that uses debhelper.
+# This file was originally written by Joey Hess and Craig Small.
+# As a special exception, when this file is copied by dh-make into a
+# dh-make output file, you may use that output file without restriction.
+# This special exception was added by Craig Small in version 0.37 of dh-make.
+
+# Uncomment this to turn on verbose mode.
+export DH_VERBOSE=1
+
+%:
+	dh $@ --buildsystem cmake 
+override_dh_auto_configure:
+	cmake ./ -DPREFIX=debian/openstructure/usr -DOPTIMIZE=ON -DCOMPOUND_LIB=compounds.chemlib
+override_dh_auto_build:
+	make -j6
+override_dh_auto_install:
+	make install
+	rm debian/openstructure/usr/bin/ldt
+	mkdir -p debian/openstructure-dev/usr
+	mv debian/openstructure/usr/include debian/openstructure-dev/usr/
+	mkdir -p debian/openstructure/usr/share/pixmaps/
+	cp modules/gui/share/images/logo-small.png debian/openstructure/usr/share/pixmaps/openstructure.png
+	mkdir -p debian/openstructure/usr/share/applications/
+	cp debian/openstructure.desktop debian/openstructure/usr/share/applications/
+	desktop-file-validate debian/openstructure/usr/share/applications/openstructure.desktop

deployment/linux/debian/debian/source/format

+3.0 (quilt)
+

deployment/linux/debian/debian/source/include-binaries

+compounds.chemlib

deployment/linux/fedora/openstructure.desktop

+[Desktop Entry]
+Name=OpenStructure
+GenericName=Open-Source Computational Structural Biology Framework
+Exec=dng
+Icon=openstructure
+Terminal=false
+Type=Application
+Categories=Science;

deployment/linux/fedora/openstructure.spec

+Name:           openstructure
+Version:        1.1 
+Release:        0.1d%{?dist}
+Summary:        Open-source computational structural biology framework
+
+
+# The entire source code is LGPLv3 except the following files:
+# modules/db/src/sqlite3.h, modules/db/src/sqlite.c
+# which have no license
+License:        LGPLv3 and unlicensed    
+URL:            www.openstructure.org 
+# The source for this package was pulled from upstream's git.  Use the
+# following commands to generate the tarball:
+#  git clone https://dng.biozentrum.unibas.ch/git/ost.git openstructure-1.1d
+#  cp /import/bc2/home/schwede/GROUP/OpenStructure/compounds.chemlib \
+#     openstructure-1.1d/
+#  tar -cJvf openstructure-1.1d.tar.xz openstructure-1.1d
+Source0: %{name}-%{version}d.tar.xz       
+Source1: %{name}.desktop
+
+BuildRequires: boost-devel,fftw-devel,eigen2-devel,libtiff-devel,libpng-devel,sip-devel,PyQt4-devel,cmake,desktop-file-utils
+Requires: sip,PyQt4     
+
+%description
+The Openstructure  project aims to provide an open-source, modular, flexible,
+molecular modelling and visualization environment. It is targeted at
+interested method developers in the field of structural bioinformatics.
+
+%prep
+%setup -n openstructure-1.1d
+
+%build
+%cmake . -DPREFIX=%{buildroot}/usr -DOPTIMIZE=ON -DCOMPOUND_LIB=compounds.chemlib
+make %{?_smp_mflags}
+
+%install
+rm -rf %{buildroot}
+make install 
+mkdir -p %{buildroot}/%{_defaultdocdir}/%{name}-%{version}
+mkdir -p %{buildroot}/%{_datadir}/pixmaps
+cp LICENSE.txt %{buildroot}/%{_defaultdocdir}/%{name}-%{version}/
+cp ReadMe.txt %{buildroot}/%{_defaultdocdir}/%{name}-%{version}/
+cp modules/gui/share/images/logo-small.png %{buildroot}/%{_datadir}/pixmaps/openstructure.png
+rm %{buildroot}/%{_bindir}/ldt
+desktop-file-install --dir=%{buildroot}/%{_datadir}/applications %{SOURCE1}
+
+%post -p /sbin/ldconfig
+
+%postun -p /sbin/ldconfig
+
+%files
+%defattr(-,root,root,-)
+%{_bindir}/*
+%{_libdir}/libost*
+%{_libdir}/openstructure
+%{_datadir}/openstructure
+%{_datadir}/applications/*
+%{_datadir}/pixmaps/*
+
+%doc
+%{_defaultdocdir}/%{name}-%{version}/LICENSE.txt
+%{_defaultdocdir}/%{name}-%{version}/ReadMe.txt
+
+%changelog
+* Wed Jul 20 2011 Valerio Mariani <valerio.mariani@unibas.ch> 1.1-1d
+- Initial release
+
+
+
+
+%package devel
+Summary:        Open-source computational structural biology framework
+Requires:       openstructure
+
+%description devel
+The Openstructure  project aims to provide an open-source, modular, flexible,
+molecular modelling and visualization environment. It is targeted at
+interested method developers in the field of structural bioinformatics.
+
+%files devel
+%{_includedir}/*
+

deployment/linux/reset_repository.py

@@ -8,7 +8,6 @@ if currdir.find('deployment')==-1 or currdir.find('linux')==-1:
   print '\n'
   sys.exit()
 
-subprocess.call('rm -fr scripts/dng.in.pre* scripts/ost_cl.in.pre*',shell=True,cwd='../../')
-subprocess.call('mv scripts/ost.in.backup scripts/ost.in',shell=True,cwd='../../')
-subprocess.call('mv scripts/dng.in.backup scripts/dng.in',shell=True,cwd='../../')
+subprocess.call('rm -fr scripts/ost_config.in.pre*',shell=True,cwd='../../')
+subprocess.call('mv scripts/ost_config.in.backup scripts/ost_config.in',shell=True,cwd='../../')