Scripts to create qmean bubndle

git-svn-id: https://dng.biozentrum.unibas.ch/svn/openstructure/trunk@2066 5a81b35b-ba03-0410-adc8-b2c5c5119f08

deployment/linux/create_qmean_bundle.py

+import os
+import shutil
+import subprocess
+import string
+import sys
+
+
+# custom parameters
+
+boost_string='\".so.1.40.0\"'
+system_python_bin='/usr/bin/python2.6'
+name_python_bin='python2.6'
+system_python_libs='/usr/lib/python2.6'
+second_system_python_libs_flag=True
+second_system_python_libs='/usr/lib/pymodules/python2.6'
+qt4_plugins='/usr/lib/qt4/plugins'
+additional_label='ubuntu'
+list_of_excluded_libraries=['ld-linux','libexpat','libgcc_s','libglib','cmov','libice','libSM','libX','libg','libGL.so','libfontconfig','libfreetype','libdrm','libxcb','libICE']
+
+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 '\n'
+print 'WARNING: If this script does not run to completion, please run the reset_repository_qmean.py script before restarting'
+print '\n'
+print 'Detecting architecture and revision'
+uname_output=subprocess.Popen('uname -a', shell=True, cwd='../../',stdout=subprocess.PIPE).stdout
+uname_line=uname_output.readlines()
+if uname_line[0].find('x86_64') !=-1:
+  libdir='lib64'
+  archstring='64bit'
+else: 
+  libdir='lib'
+  archstring='32bit'
+svninfo_output=subprocess.Popen('svn info', shell=True, cwd='../../',stdout=subprocess.PIPE).stdout
+svninfo_lines=svninfo_output.readlines()
+svninfo_split=string.split(svninfo_lines[4])
+revstring=svninfo_split[1]
+directory_name='qmean-'+archstring+'-'+additional_label+'-rev'+revstring
+print 'Stripping subversion information to avoid accidental commit'
+subprocess.call('rm -rf $(find . -name .svn)',shell=True,cwd='../../')
+print 'Tweaking scripts for bundle use'
+subprocess.call('mv scripts/ost.in scripts/ost.in.backup',shell=True,cwd='../../')
+subprocess.call('sed "s/@PYTHON_BINARY@/\$DNG_ROOT\/bin\/'+name_python_bin+'/g" scripts/ost.in.backup > scripts/ost.in.preprepre',shell=True,cwd='../../')
+subprocess.call('sed "s/\#export LD_LIBRARY_PATH/ export LD_LIBRARY_PATH/g" scripts/ost.in.preprepre > scripts/ost.in.prepre',shell=True,cwd='../../')
+subprocess.call('sed "s/\#export PYTHONHOME/ export PYTHONHOME/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 modules/scratch/qmean/scripts/qmean.in modules/scratch/qmean/scripts/qmean.in.backup',shell=True,cwd='../../')
+subprocess.call('sed "s/@PYTHON_BINARY@/\$DNG_ROOT\/bin\/'+name_python_bin+'/g" modules/scratch/qmean/scripts/qmean.in.backup > modules/scratch/qmean/scripts/qmean.in.preprepre',shell=True,cwd='../../')
+subprocess.call('sed "s/\#export LD_LIBRARY_PATH/ export LD_LIBRARY_PATH/g" modules/scratch/qmean/scripts/qmean.in.preprepre > modules/scratch/qmean/scripts/qmean.in.prepre',shell=True,cwd='../../')
+subprocess.call('sed "s/\#export PYTHONHOME/ export PYTHONHOME/g" modules/scratch/qmean/scripts/qmean.in.prepre > modules/scratch/qmean/scripts/qmean.in.pre',shell=True,cwd='../../')
+subprocess.call('sed "s/\#export QT_PLUGIN_PATH/ export QT_PLUGIN_PATH/g" modules/scratch/qmean/scripts/qmean.in.pre > modules/scratch/qmean/scripts/qmean.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.prepre',shell=True,cwd='../../')
+subprocess.call('sed "s/\#export PYTHONHOME/ export PYTHONHOME/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='../../')
+print 'Compiling Openstructure/Qmean'
+subprocess.call('cmake ./ -DCMAKE_BUILD_TYPE=Release -DPREFIX='+directory_name+' -DBoost_COMPILER='+boost_string+' -DONLY_QMEAN=ON -DENABLE_IMG=OFF -DENABLE_UI=OFF -DENABLE_GFX=OFF -DCOMPOUND_LIB=ChemLib/compounds.chemlib', shell=True,cwd='../../')
+subprocess.call('make',shell=True,cwd='../../')
+print 'Removing obsolete packages and package directory'
+subprocess.call('rm -fr qmean-*',shell=True,cwd='../../')
+print 'Creating new package directory'
+subprocess.call('mkdir '+directory_name,shell=True,cwd='../../')
+subprocess.call('mkdir '+directory_name+'/bin',shell=True,cwd='../../')
+so_list=[]
+print 'Creating new dependency list'
+walk_list=os.walk('../../stage')
+for dir_entry in walk_list:
+  for file_entry in dir_entry[2]:
+    if file_entry.find('.so')==len(file_entry)-3 or file_entry=='gosty':
+      filepath=os.path.join(dir_entry[0],file_entry)
+      so_list.append(filepath)  
+dep_list=[]
+for so_entry in so_list:
+   dep=subprocess.Popen('perl ./ldd-rec.pl '+so_entry,shell=True,stdout=subprocess.PIPE,cwd='./').stdout
+   dep_so_entry=dep.readlines()
+   for dep_entry in dep_so_entry:
+     dep_list.append(dep_entry[:-1]) 
+sorted_dep_list=sorted(list(set(dep_list)))
+print 'Filtering system libraries from depenedency list'
+filtered_dep_list=[]
+for entry in sorted_dep_list:
+   exclude=False
+   for exclusion in list_of_excluded_libraries:
+     if entry.find(exclusion)!=-1:
+       exclude=True
+   if exclude==False: 
+     filtered_dep_list.append(entry)
+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',shell=True,cwd='../../')
+print 'Copy python libraries into package directory structure'
+subprocess.call('cp -pRL '+system_python_libs+' '+directory_name+'/'+libdir,shell=True,cwd='../../')
+if second_system_python_libs_flag==True:
+  subprocess.call('cp -pRL '+second_system_python_libs+'/* '+directory_name+'/'+libdir+'/'+name_python_bin,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 'Copy examples into package directory structure'
+subprocess.call('cp -pRL  examples  '+directory_name+'/share/openstructure/',shell=True,cwd='../../')
+print 'Removing headers from package directory structure'
+subprocess.call('rm -fr   '+directory_name+'/include',shell=True,cwd='../../')
+print 'Copy qmean examples into package directory structure'
+subprocess.call('cp -pRL  modules/scratch/qmean/examples '+directory_name+'',shell=True,cwd='../../')
+print 'Copy readme and license files into package directory structure'
+subprocess.call('cp -pRL  modules/scratch/qmean/LICENSE.txt '+directory_name+'',shell=True,cwd='../../')
+subprocess.call('cp -pRL  modules/scratch/qmean/README.txt '+directory_name+'',shell=True,cwd='../../')
+print 'Resetting script to non-bundle versions'
+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 modules/scratch/qmean/scripts/qmean.in',shell=True,cwd='../../')
+subprocess.call('rm modules/scratch/qmean/scripts/qmean.in.pre*',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('mv modules/scratch/qmean/scripts/qmean.in.backup modules/scratch/qmean/scripts/qmean.in',shell=True,cwd='../../')
+subprocess.call('tar cfz '+directory_name+'.tgz '+directory_name,shell=True,cwd='../../')
+

deployment/linux/reset_repository.py

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

deployment/linux/reset_repository_qmean.py

+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/dng.in.pre* scripts/ost_cl.in.pre* modules/scratch/qmean/scripts/qmean.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('mv modules/scratch/qmean/scripts/qmean.in.backup scripts/dng.in modules/scratch/qmean/scripts/qmean.in',shell=True,cwd='../../')
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