New bundling script

Removed the directories with scripts to create rpm and deb as in the future we will use Andi's cpack

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

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."
 

deployment/linux/create_bundle_alt.py

-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')

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}/*
-