From 81a2454a9abde6bb79793eb4c72e4a8725f5fe7f Mon Sep 17 00:00:00 2001
From: Christoph Helma <helma@in-silico.ch>
Date: Sat, 15 Aug 2015 11:21:26 +0200
Subject: initial installation script

---
 ext/lazar/extconf.rb | 88 ++++++++++++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 88 insertions(+)
 create mode 100644 ext/lazar/extconf.rb

diff --git a/ext/lazar/extconf.rb b/ext/lazar/extconf.rb
new file mode 100644
index 0000000..738a85b
--- /dev/null
+++ b/ext/lazar/extconf.rb
@@ -0,0 +1,88 @@
+require 'fileutils'
+main_dir = File.expand_path(File.join(File.dirname(__FILE__),"..",".."))
+
+# install OpenBabel
+
+require 'mkmf'
+require 'rbconfig'
+require 'openbabel/version'
+
+openbabel_version = 2.3.2
+
+openbabel_dir = File.join main_dir, "openbabel"
+src_dir = File.join openbabel_dir, "openbabel-#{openbabel_version}"
+build_dir = File.join openbabel_dir, "build"
+install_dir = openbabel_dir 
+install_lib_dir = File.join install_dir, "lib"
+lib_dir = File.join openbabel_dir, "lib", "openbabel"
+ruby_src_dir = File.join src_dir, "scripts", "ruby"
+
+begin
+  nr_processors = `grep processor /proc/cpuinfo | wc -l` # speed up compilation, Linux only
+rescue
+  nr_processors = 1
+end
+
+Dir.chdir openbabel_dir do
+  FileUtils.rm_rf src_dir
+  puts "Downloading OpenBabel sources"
+  system "curl -L -d use_mirror=netcologne 'http://downloads.sourceforge.net/project/openbabel/openbabel/#{ob_num_ver}/openbabel-#{ob_num_ver}.tar.gz' | tar xz"
+  system "sed -i -e 's/-Wl,-flat_namespace//;s/-flat_namespace//' #{File.join ruby_src_dir, "extconf.rb"}" # remove unrecognized compiler option
+  system "sed -i -e 's/Init_OpenBabel/Init_openbabel/g' #{File.join ruby_src_dir,"*cpp"}" # fix swig bindings
+  system "sed  -i -e 's/Config::CONFIG/RbConfig::CONFIG/' #{File.join src_dir, "scripts", "CMakeLists.txt" }" # fix Ruby Config
+  system "sed  -i -e 's/Config::CONFIG/RbConfig::CONFIG/' #{File.join ruby_src_dir, "extconf.rb" }" # fix Ruby Config
+end
+FileUtils.mkdir_p build_dir
+FileUtils.mkdir_p install_dir
+Dir.chdir build_dir do
+  puts "Configuring OpenBabel"
+  cmake = "cmake #{src_dir} -DCMAKE_INSTALL_PREFIX=#{install_dir} -DBUILD_GUI=OFF -DENABLE_TESTS=OFF -DRUBY_BINDINGS=ON"
+  # set rpath for local installations
+  # http://www.cmake.org/Wiki/CMake_RPATH_handling
+  # http://vtk.1045678.n5.nabble.com/How-to-force-cmake-not-to-remove-install-rpath-td5721193.html
+  cmake += " -DCMAKE_INSTALL_RPATH:STRING=\"#{install_lib_dir}\"" 
+  system cmake
+end
+
+# local installation in gem directory
+Dir.chdir build_dir do
+  puts "Compiling OpenBabel sources."
+  system "make -j#{nr_processors}"
+  system "make install"
+  ENV["PKG_CONFIG_PATH"] = File.dirname(File.expand_path(Dir["#{install_dir}/**/openbabel*pc"].first))
+end
+
+# get include and lib from pkg-config
+ob_include=`pkg-config openbabel-2.0 --cflags-only-I`.sub(/\s+/,'').sub(/-I/,'')
+ob_lib=`pkg-config openbabel-2.0 --libs-only-L`.sub(/\s+/,'').sub(/-L/,'')
+
+# compile ruby bindings
+puts "Compiling and installing OpenBabel Ruby bindings."
+Dir.chdir ruby_src_dir do
+  # fix rpath
+  system "sed -i 's|with_ldflags.*$|with_ldflags(\"#\$LDFLAGS -dynamic -Wl,-rpath,#{install_lib_dir}\") do|' #{File.join(ruby_src_dir,'extconf.rb')}"
+  system "#{RbConfig.ruby} extconf.rb --with-openbabel-include=#{ob_include} --with-openbabel-lib=#{ob_lib}"
+  system "make -j#{nr_processors}"
+end
+FileUtils.cp(ruby_src_dir+"/openbabel.#{RbConfig::CONFIG["DLEXT"]}", "./")
+FileUtils.mkdir_p lib_dir
+FileUtils.mv "openbabel.#{RbConfig::CONFIG["DLEXT"]}" lib_dir
+FileUtils.remove_entry_secure src_dir, build_dir
+
+# install fminer
+fminer_dir = File.join main_dir, "libfminer"
+system "git clone git://github.com/amaunz/fminer2.git #{fminer_dir}"
+
+["libbbrc","liblast"].each do |lib|
+  FileUtils.cd File.join(fminer_dir,lib)
+  system "sed -i 's,^INCLUDE_OB.*,INCLUDE_OB\ =\ #{ob_include},g' Makefile" 
+  system "sed -i 's,^LDFLAGS_OB.*,LDFLAGS_OB\ =\ #{ob_lib},g' Makefile"
+  system "sed -i 's,^INCLUDE_RB.*,INCLUDE_RB\ =\ #{RbConfig::CONFIG['rubyhdrdir']},g' Makefile" 
+  system "make ruby"
+end
+
+# install last-utils
+FileUtils.cd main_dir
+"git clone git://github.com/amaunz/last-utils.git"
+
+# install R packagemain_dir
-- 
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