diff --git a/deployment/linux/README.txt b/deployment/linux/README.txt index 2f1ab3010a1c0854b08e58e45337296f3fe4938a..02beeb3f36f18f170a6b1c4768120552ff2c1c70 100644 --- a/deployment/linux/README.txt +++ b/deployment/linux/README.txt @@ -3,4 +3,5 @@ HOW TO USE THE BUNDLE SCRIPTS: 1. Checkout a copy of the OpenStructure repository. 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 +4. If the process stops without completing, reset the repository with 'git +reset --hard HEAD' from the top level directory diff --git a/deployment/linux/create_bundle.py b/deployment/linux/create_bundle.py index 3f04533f0c4d6c3f84e907a0f73099bdf5988929..b59409ffffc7d099c31f7d8437eae8a72e49e50a 100644 --- a/deployment/linux/create_bundle.py +++ b/deployment/linux/create_bundle.py @@ -4,31 +4,56 @@ import subprocess import string import sys import datetime +import sip +import PyQt4 -# custom parameters +# parameters that can be modified +qt4_plugins_location='/usr/lib/i386-linux-gnu/qt4/plugins' +ssl_crypto_location='/lib/i386-linux-gnu/' +chemlib_dictionary_location='/home/bundler/compounds.chemlib' +list_of_excluded_libraries=[ +'ld-linux', +'libexpat', +'libgcc_s', +'libglib', +'cmov', +'libice', +'libSM', +'libX', +'libg', +'libGL.so', +'libfontconfig', +'libfreetype', +'libdrm', +'libxcb', +'libICE', +'libnvidia', +'libc' +] -if len(sys.argv) < 3: - print 'usage: create_bundle.py additional_label system_python_version' +if len(sys.argv) < 2: + print 'usage: create_bundle.py additional_label' sys.exit() -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 -second_system_python_libs='/usr/lib/pymodules/'+system_python_version -python_bin_in_bundle='python' -qt4_plugins='/usr/lib/qt4/plugins' additional_label=sys.argv[1] -list_of_excluded_libraries=['ld-linux','libexpat','libgcc_s','libglib','cmov','libice','libSM','libX','libg','libGL.so','libfontconfig','libfreetype','libdrm','libxcb','libICE','libnvidia','libc'] + currdir=os.getcwd() if currdir.find('deployment')==-1 or currdir.find('linux')==-1: print '\n' print 'ERROR: Please run this script from the deployment/linux directory' print '\n' sys.exit() + +print "WARNING: If this script does not run to completion, please run 'git reset --hard HEAD' in the main directory (two up from here) before restarting" + +system_python_version=sys.version_info +system_python_executable='python'+str(system_python_version[0])+'.'+str(system_python_version[1]) +system_python_bin='/usr/bin/'+system_python_executable +system_python_libs='/usr/lib/'+system_python_executable +qt4_module_location=os.path.dirname(PyQt4.__file__) +sip_module_location=os.path.dirname(sip.__file__) print '\n' -print 'WARNING: If this script does not run to completion, please run the reset_repository.py script before restarting' print '\n' print 'Detecting architecture and revision' uname_output=subprocess.Popen('uname -a', shell=True, cwd='../../',stdout=subprocess.PIPE).stdout @@ -39,26 +64,16 @@ if uname_line[0].find('x86_64') !=-1: else: libdir='lib' archstring='32bit' -date_pattern='%Y-%b-%d' -build=datetime.date.today() -directory_name='openstructure-linux-'+archstring+'-'+additional_label+'-'+str(build) +directory_name='openstructure-linux-'+archstring+'-'+additional_label print 'Hardcoding package python binary path in openstructure executables' +subprocess.call('rm -f scripts/ost_config.in.pre* scripts/ost_config.in.backup',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/@PYTHON_BINARY@/\$DNG_ROOT\/bin\/python/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 'Compiling Openstructure' -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('cmake ./ -DCMAKE_BUILD_TYPE=Release -DPREFIX='+directory_name+' -DCOMPOUND_LIB='+chemlib_dictionary_location+' -DENABLE_IMG=ON -DENABLE_GUI=ON -DENABLE_GFX=ON -DOPTIMIZE=ON',shell=True,cwd='../../') subprocess.call('make -j2',shell=True,cwd='../../') print 'Removing obsolete packages and package directory' subprocess.call('rm -fr openstructure-linux*',shell=True,cwd='../../') @@ -66,14 +81,12 @@ 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+'/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+'/python/',shell=True,cwd='../../') - subprocess.call('cp -pRL '+second_system_python_libs+'/PyQt* stage/'+libdir+'/python/',shell=True,cwd='../../') +subprocess.call('cp -pRL '+system_python_libs+' stage/'+libdir+'/',shell=True,cwd='../../') +subprocess.call('rm -fr stage/'+libdir+'/'+system_python_executable+'/dist-packages',shell=True,cwd='../../') +subprocess.call('cp -pRL '+sip_module_location+'/sip* stage/'+libdir+'/'+system_python_executable+'/',shell=True,cwd='../../') +subprocess.call('cp -pRL '+qt4_module_location+' stage/'+libdir+'/'+system_python_executable+'/',shell=True,cwd='../../') print 'Creating new dependency list' so_list=[] walk_list=os.walk('../../stage') @@ -106,13 +119,12 @@ for entry in filtered_dep_list: 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+'/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+'/python/',shell=True,cwd='../../') - subprocess.call('cp -pRL '+second_system_python_libs+'/PyQt* '+directory_name+'/'+libdir+'/python/',shell=True,cwd='../../') +subprocess.call('cp -pRL '+system_python_libs+' '+directory_name+'/'+libdir+'/'+system_python_executable+'/',shell=True,cwd='../../') +subprocess.call('rm -fr '+directory_name+'/'+libdir+'/'+system_python_executable+'/dist-packages',shell=True,cwd='../../') +subprocess.call('cp -pRL '+sip_module_location+'/sip* '+directory_name+'/'+libdir+'/'+system_python_executable+'/',shell=True,cwd='../../') +subprocess.call('cp -pRL '+qt4_module_location+' '+directory_name+'/'+libdir+'/'+system_python_executable+'/',shell=True,cwd='../../') print 'Copy Qt 4 plugins into package directory structure' -subprocess.call('cp -pRL '+qt4_plugins+' '+directory_name+'/bin/',shell=True,cwd='../../') +subprocess.call('cp -pRL '+qt4_plugins_location+' '+directory_name+'/bin/',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' @@ -122,19 +134,19 @@ subprocess.call('cp deployment/README.html '+directory_name,shell=True,cwd='../. print 'Creating executables at the top level of the package directory structure' subprocess.call('ln -sf bin/dng ./dng',shell=True,cwd='../../'+directory_name) subprocess.call('ln -sf bin/ost ./ost',shell=True,cwd='../../'+directory_name) +subprocess.call('ln -sf bin/lddt ./lddt',shell=True,cwd='../../'+directory_name) print 'Copying additional libraries in the package directory structure' -subprocess.call('cp /usr/lib/libssl.so.0.9.8 '+directory_name+'/'+libdir,shell=True,cwd='../../') -subprocess.call('cp /usr/lib/libcrypto.so.0.9.8 '+directory_name+'/'+libdir,shell=True,cwd='../../') -print 'Removing headers from package directory structure' -subprocess.call('rm -fr '+directory_name+'/include',shell=True,cwd='../../') +subprocess.call('cp '+ssl_crypto_location+'/libssl.so* '+directory_name+'/'+libdir,shell=True,cwd='../../') +subprocess.call('cp '+ssl_crypto_location+'/libcrypto.so* '+directory_name+'/'+libdir,shell=True,cwd='../../') +print 'Copying python headers in the package directory structure' +subprocess.call('mkdir -p '+directory_name+'/local/include/',shell=True,cwd='../../') +subprocess.call('cp -r /usr/include/'+system_python_executable+' '+directory_name+'/local/include/',shell=True,cwd='../../') print 'Stripping pyc files from bundle' subprocess.call('rm -rf $(find . -name *.pyc)',shell=True,cwd='../../') 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_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='../../') +print 'Compressing the bundle' subprocess.call('tar cfz '+directory_name+'.tgz '+directory_name,shell=True,cwd='../../') +print "Done. Please run 'git reset --hard HEAD' in the top directory before restarting." diff --git a/deployment/linux/create_bundle_alt.py b/deployment/linux/create_bundle_alt.py deleted file mode 100755 index 6e5cf9bcf26311b4d7e1acd2ee61a18b9fc36a9f..0000000000000000000000000000000000000000 --- a/deployment/linux/create_bundle_alt.py +++ /dev/null @@ -1,183 +0,0 @@ -import os,os.path -import shutil -import sys -import tarfile -import subprocess -import re - -def get_libdir(): - machine=os.uname()[4] - if machine.find('x86_64') !=-1: - return 'lib64' - else: - return 'lib' - -def get_arch(): - machine=os.uname()[4] - if machine.find('x86_64') !=-1: - return '64bit' - else: - return '32bit' - -def clean(standalonedir): - if os.path.exists(standalonedir): - shutil.rmtree(standalonedir) - -def copy_stage(stagedir,standalonedir): - libdir=get_libdir() - copytree_ex(os.path.join(stagedir,'bin'),os.path.join(standalonedir,'bin')) - copytree_ex(os.path.join(stagedir,libdir),os.path.join(standalonedir,libdir)) - if os.path.exists(os.path.join(stagedir,'share')): - copytree_ex(os.path.join(stagedir,'share'),os.path.join(standalonedir,'share')) - -def collect_deps(binaries,exclude_list): - dependencies=set() - for binary in binaries: - collect_deps_recursive_(binary,dependencies,exclude_list) - return dependencies - -def collect_deps_recursive_(binary,collected,exclude_list): - ldd_stdout=subprocess.Popen(['ldd',binary],stdout=subprocess.PIPE).stdout - output=ldd_stdout.readlines() - new_dependencies=set() - for entry in output: - if entry.find("statically linked")!=-1: - continue - sp=entry.split('(0x') - if len(sp)>0: # only continue if line is dependency - sp2=sp[0].split('=>',1)[-1].split() - if sp2: #ensure libname exists (fix for virtual linux-gate) - text=sp2[0] - if not text.split('.')[0].split('/')[-1] in exclude_list and not text in collected: - collect_deps_recursive_(text,collected,exclude_list) - collected.add(text) - - -def copy_deps(binaries,standalonedir,exclude_list): - dependencies=set() - walk_list=os.walk(standalonedir) - binaries_list=[] - for dir_entry in walk_list: - for file_entry in dir_entry[2]: - if file_entry.endswith('.so') or file_entry in binaries: - filepath=os.path.join(dir_entry[0],file_entry) - binaries_list.append(filepath) - dependencies=collect_deps(binaries_list,exclude_list) - for dep in dependencies: - shutil.copy2(dep,os.path.join(standalonedir,get_libdir())) - -def copy_examples(stagedir): - #todo - pass -def copy_qt_plugins(): - #todo - pass - -def process_scripts(scripts,standalonedir): - for script in scripts: - fp=open(os.path.join(standalonedir,'bin',script),'r') - text=fp.read() - fp.close() - text=re.sub('#export PYTHONPATH','export PYTHONPATH',text) - fp=open(os.path.join(standalonedir,'bin',script),'w') - fp.write(text) - fp.close() - -def create_package(name,standalonedir): - try: - import pysvn - try: - client=pysvn.Client() - svn_info=client.info('.') - revstring='-rev'+str(svn_info['revision'.number]) - except pysvn.ClientError: - print 'No svn directory found. Addin no revision number.' - revstring='' - except ImportError: - print 'Pysvn not installed. Adding no revision number.' - revstring='' - tar_name=name+'-linux-'+get_arch()+revstring+'.tgz' - if os.path.exists(tar_name): - os.remove(tar_name) - tar = tarfile.open(tar_name, "w:gz") - tar.add(standalonedir,name+'-linux-'+get_arch()+revstring) - tar.close() - -def ignorer(dirpath,files): - ignores=[] - for f in files: - base=os.path.splitext(f)[0] - if f.endswith('.py'): - if base+'.pyc' in files or base+'.pyo' in files: - ignores.append(f) - elif f.endswith('.pyc'): - if base+'.pyo' in files: - ignores.append(f) - return ignores - -def copy_python_dirs(standalonedir): - dirs=sys.path[1:] - dirs.sort() #get toplevel dir to the beginning - toplevel=dirs[0] - shutil.copytree(toplevel,os.path.join(standalonedir,get_libdir(),'python'),ignore=ignorer) - for d in dirs[1:]: - if not d.startswith(toplevel) and os.path.isdir(d): - toplevel=d - copytree_ex(toplevel,os.path.join(standalonedir,get_libdir(),'python'),ignore=ignorer) - - -def copytree_ex(source,destination, symlinks=False,ignore=None): - if not os.path.exists(destination): - shutil.copytree(source,destination,symlinks,ignore) - elif os.path.isdir(destination): - files=os.listdir(source) - if ignore: - ignores=ignore(source,files) - else: - ignores=[] - for f in files: - srcname=os.path.join(source,f) - dstname=os.path.join(destination,f) - if os.path.isdir(os.path.join(source,f)): - copytree_ex(srcname,dstname,symlinks,ignore=ignorer) - elif f not in ignores: - if symlinks and os.path.islink(srcname): - linkto = os.readlink(srcname) - os.symlink(linkto, dstname) - else: - shutil.copy2(srcname, dstname) - else: - raise IOError("destination is not a directory") - - - -############ main script #################### - -stagedir='../../stage' -ost_stagedir='../../../openstructure/stage' -standalonedir=os.path.join(os.getcwd(),'standalone') -binaries=['gosty'] -exclude_list=['ld-linux','libexpat','libgcc_s','libglib','cmov','libice','libSM','libX','libg','libGL','libfontconfig','libfreetype','libdrm','libxcb','libICE'] -scripts=['dng','ost'] - -#compile_stage() - -clean(standalonedir) -print 'copying stage' -copy_stage(stagedir,standalonedir) -print 'copying ost stage' -copy_stage(ost_stagedir,standalonedir) -print 'copying python' -shutil.copy(sys.executable,os.path.join(stagedir,'bin')) -copy_python_dirs(standalonedir) -print 'copying dependencies' -binaries.append(sys.executable) -copy_deps(binaries,standalonedir,exclude_list) -print 'copying examples' -copy_examples(stagedir) -print 'copying plugins' -copy_qt_plugins() -print 'processing scripts' -process_scripts(scripts,standalonedir) -print 'creating package' -create_package('openstructure','standalone') diff --git a/deployment/linux/debian/README b/deployment/linux/debian/README deleted file mode 100644 index c3a5a886f2754202845d533c5399e6eeb416ae86..0000000000000000000000000000000000000000 --- a/deployment/linux/debian/README +++ /dev/null @@ -1,8 +0,0 @@ -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 diff --git a/deployment/linux/debian/debian/README.source b/deployment/linux/debian/debian/README.source deleted file mode 100644 index c6c09893537f7e95bd2a01b7fe343ed65798ecf3..0000000000000000000000000000000000000000 --- a/deployment/linux/debian/debian/README.source +++ /dev/null @@ -1,18 +0,0 @@ -===============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 =================================== diff --git a/deployment/linux/debian/debian/changelog b/deployment/linux/debian/debian/changelog deleted file mode 100644 index 9ecfb662316dd8c2d6a8e6ddcc17e4cf3573e526..0000000000000000000000000000000000000000 --- a/deployment/linux/debian/debian/changelog +++ /dev/null @@ -1,5 +0,0 @@ -openstructure (1.1d-0ubuntu1) natty; urgency=low - - * Initial release - - -- Valerio Mariani <valerio.mariani@unibas.ch> Wed, 13 Jul 2011 15:41:35 +0200 diff --git a/deployment/linux/debian/debian/chemdict_tool.1 b/deployment/linux/debian/debian/chemdict_tool.1 deleted file mode 100644 index 7cbb4e805d2f7e52bf0ae16701d208cc5946fff1..0000000000000000000000000000000000000000 --- a/deployment/linux/debian/debian/chemdict_tool.1 +++ /dev/null @@ -1,33 +0,0 @@ -.\" 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. diff --git a/deployment/linux/debian/debian/compat b/deployment/linux/debian/debian/compat deleted file mode 100644 index 7f8f011eb73d6043d2e6db9d2c101195ae2801f2..0000000000000000000000000000000000000000 --- a/deployment/linux/debian/debian/compat +++ /dev/null @@ -1 +0,0 @@ -7 diff --git a/deployment/linux/debian/debian/control b/deployment/linux/debian/debian/control deleted file mode 100644 index 43a9f02fdda663dcf358819cf3bb92381c501311..0000000000000000000000000000000000000000 --- a/deployment/linux/debian/debian/control +++ /dev/null @@ -1,23 +0,0 @@ -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. diff --git a/deployment/linux/debian/debian/copyright b/deployment/linux/debian/debian/copyright deleted file mode 100644 index b93d7503fb504646b3023bcc25817335d2579868..0000000000000000000000000000000000000000 --- a/deployment/linux/debian/debian/copyright +++ /dev/null @@ -1,40 +0,0 @@ -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. diff --git a/deployment/linux/debian/debian/dng.1 b/deployment/linux/debian/debian/dng.1 deleted file mode 100644 index dbc68330d425affad81420e25645719ac07c8b24..0000000000000000000000000000000000000000 --- a/deployment/linux/debian/debian/dng.1 +++ /dev/null @@ -1,39 +0,0 @@ -.\" 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 diff --git a/deployment/linux/debian/debian/openstructure.desktop b/deployment/linux/debian/debian/openstructure.desktop deleted file mode 100644 index b5ae761af421073b92e3ce58fa0c5100417a3ae8..0000000000000000000000000000000000000000 --- a/deployment/linux/debian/debian/openstructure.desktop +++ /dev/null @@ -1,8 +0,0 @@ -[Desktop Entry] -Name=OpenStructure -GenericName=Open-Source Computational Structural Biology Framework -Exec=dng -Icon=openstructure -Terminal=false -Type=Application -Categories=Education;Science; diff --git a/deployment/linux/debian/debian/openstructure.manpages b/deployment/linux/debian/debian/openstructure.manpages deleted file mode 100644 index e73d09dbbec1bf1adaed4065f926ecbe8e872771..0000000000000000000000000000000000000000 --- a/deployment/linux/debian/debian/openstructure.manpages +++ /dev/null @@ -1,3 +0,0 @@ -debian/ost.1 -debian/dng.1 -debian/chemdict_tool.1 diff --git a/deployment/linux/debian/debian/ost.1 b/deployment/linux/debian/debian/ost.1 deleted file mode 100644 index afd5f75dcb8eadc27a09ecacb147138c3451ac7a..0000000000000000000000000000000000000000 --- a/deployment/linux/debian/debian/ost.1 +++ /dev/null @@ -1,18 +0,0 @@ -.\" 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] diff --git a/deployment/linux/debian/debian/postinst b/deployment/linux/debian/debian/postinst deleted file mode 100644 index a448189622f2efd26b94eb33f2759706a6d7bdbd..0000000000000000000000000000000000000000 --- a/deployment/linux/debian/debian/postinst +++ /dev/null @@ -1,40 +0,0 @@ -#!/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 diff --git a/deployment/linux/debian/debian/rules b/deployment/linux/debian/debian/rules deleted file mode 100755 index 7b9d18ba98b725099155c5f3d87a78f20e2cba5c..0000000000000000000000000000000000000000 --- a/deployment/linux/debian/debian/rules +++ /dev/null @@ -1,27 +0,0 @@ -#!/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 diff --git a/deployment/linux/debian/debian/source/format b/deployment/linux/debian/debian/source/format deleted file mode 100644 index c3d9f2407417795889250717d7b519eadd8373e6..0000000000000000000000000000000000000000 --- a/deployment/linux/debian/debian/source/format +++ /dev/null @@ -1,2 +0,0 @@ -3.0 (quilt) - diff --git a/deployment/linux/debian/debian/source/include-binaries b/deployment/linux/debian/debian/source/include-binaries deleted file mode 100644 index e2a64033aea5f1dda66b509afe7ee03c8d40095e..0000000000000000000000000000000000000000 --- a/deployment/linux/debian/debian/source/include-binaries +++ /dev/null @@ -1 +0,0 @@ -compounds.chemlib diff --git a/deployment/linux/fedora/openstructure.desktop b/deployment/linux/fedora/openstructure.desktop deleted file mode 100644 index 5da5cfab6fa466c91de1e5be5cf5073448ad72dd..0000000000000000000000000000000000000000 --- a/deployment/linux/fedora/openstructure.desktop +++ /dev/null @@ -1,8 +0,0 @@ -[Desktop Entry] -Name=OpenStructure -GenericName=Open-Source Computational Structural Biology Framework -Exec=dng -Icon=openstructure -Terminal=false -Type=Application -Categories=Science; diff --git a/deployment/linux/fedora/openstructure.spec b/deployment/linux/fedora/openstructure.spec deleted file mode 100644 index 3d27b5deac2b8e299e1ab1406900a722347866be..0000000000000000000000000000000000000000 --- a/deployment/linux/fedora/openstructure.spec +++ /dev/null @@ -1,82 +0,0 @@ -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}/* - diff --git a/deployment/linux/reset_repository.py b/deployment/linux/reset_repository.py deleted file mode 100644 index 6ac0809e34a767ff7ff16febd6d392b95e31861f..0000000000000000000000000000000000000000 --- a/deployment/linux/reset_repository.py +++ /dev/null @@ -1,13 +0,0 @@ -import subprocess -import os - -currdir=os.getcwd() -if currdir.find('deployment')==-1 or currdir.find('linux')==-1: - print '\n' - print 'ERROR: Please run this script from the deployment/linux directory' - print '\n' - sys.exit() - -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='../../') -