New install-script(tested on Ubuntu 9.10/8.10)

1 files changed, 363 insertions, 0 deletions

diff --git a/bin/opentox-install-ubuntu.sh b/bin/opentox-install-ubuntu.sh
new file mode 100755
index 0000000..e038c17
--- /dev/null
+++ b/bin/opentox-install-ubuntu.sh
@@ -0,0 +1,363 @@
+#!/bin/bash
+#Installation is tested on Debian Ubuntu 9.10
+#Update the system
+
+FAILED=0
+STARTPATH=$PWD
+ERRLOG=$PWD/'install_err.log'
+INSTALLLOG=$PWD/'install_log.log'
+DATE=$(date +%Y/%m/%d\ %H:%M:%S)
+BRANCH=$1
+GEMVERSION="1.3.5"
+GITVERSION="1.6.5.2"
+RAPTORVERSION="1.4.20"
+RASQALVERSION="0.9.16"
+RASQALVERSION2="0.9.15"
+REDLANDVERSION="1.0.7"
+REDBINDVERSION="1.0.7.1"
+
+if [ "$BRANCH" = '' ]
+then
+  echo "Please enter: sudo ./[filename] [brunchtpy]"
+  exit 1
+fi
+echo "================================================="
+echo "Selected branch is: $BRANCH"
+echo "================================================="
+echo "Please enshure that the sudo package is installed"
+echo "on your system. "
+echo "On Ubuntu Linux sudo is installed by default."
+echo "If you are unsure check with it 'sudo ls'"
+echo "and installed it with 'apt-get install sudo'"
+echo "and add your username with visudo."
+echo "================================================="
+echo "Some programs and the OpenTox webservices will be installed in the current folder."
+echo "================================================="
+echo -n "To continue installation press y: "
+read answer
+if [ "$answer" != "y" ]
+then
+  echo "exiting the script..."
+  exit 1
+fi
+
+echo "opentox webservice install log - " $DATE > $INSTALLLOG
+echo "opentox webservice install err log - " $DATE > $ERRLOG
+echo "Installing: build-essential"
+sudo apt-get install build-essential  | tee -a $INSTALLLOG
+
+echo "Installing: ruby 1.8 with its dev files"
+sudo apt-get install ruby ruby1.8-dev  | tee -a $INSTALLLOG
+
+echo "Installing: gems rdoc rubygems libxml-parser-ruby1.8 libxml++2.6-dev libyaml-ruby libzlib-ruby sqlite3 libsqlite3-dev libsqlite3-ruby1.8 and rake"
+sudo apt-get install gems rdoc rubygems libxml-parser-ruby1.8 libxml++2.6-dev libyaml-ruby libzlib-ruby rake sqlite3 libsqlite3-dev libsqlite3-ruby1.8 | tee -a $INSTALLLOG  
+
+#RUBYGEMS
+echo "Installing rubygems from source. This may take some time"
+if [ ! -d $STARTPATH/rubygems-$GEMVERSION ]; 
+then
+	wget http://rubyforge.org/frs/download.php/60718/rubygems-$GEMVERSION.tgz >>$INSTALLLOG 2>>$ERRLOG 
+	tar xzfv rubygems-$GEMVERSION.tgz  >>$INSTALLLOG 2>>$ERRLOG
+	cd rubygems-$GEMVERSION  
+	sudo ruby setup.rb  >>$INSTALLLOG 2>>$ERRLOG
+	cd ..
+	sudo rm rubygems-$GEMVERSION.tgz  
+	CHECKGEM=`gem -v` 
+	if [ "$CHECKGEM"  == "$GEMVERSION" ]
+	then
+		echo "Adding http://gems.github.com to ruby gem sources"
+		sudo gem sources -a http://gems.github.com  >>$INSTALLLOG 2>>$ERRLOG
+
+		echo "================================================="
+		echo "Rubygems version $GEMVERSION successfully installed."
+		echo "================================================="
+	else
+	    echo "Rubygems version $GEMVERSION installation failed."
+	    FAILED=1
+	fi
+else
+	echo "rubygems-$GEMVERSION folder already exist. "
+fi
+
+echo "Installing packages: zlib1g-dev tcl curl perl ssh tcl tk8.5 libopenssl-ruby libgsl0-dev swig r-base rinruby"
+sudo apt-get install zlib1g-dev tcl curl perl libopenssl-ruby libgsl0-dev r-base | tee -a $INSTALLLOG
+sudo apt-get install ssh tcl tk8.5 | tee -a $INSTALLLOG
+sudo apt-get install swig | tee -a $INSTALLLOG
+
+#echo "Installing gems jeweler sinatra emk-sinatra-url-for dm-core cehoffman-sinatra-respond_to rest-client rack-contrib thin cucumber datamapper data_objects do_sqlite3 rinruby"
+#sudo gem install jeweler  | tee -a $INSTALLLOG
+#sudo gem install sinatra | tee -a $INSTALLLOG
+#sudo gem install emk-sinatra-url-for -s http://gems.github.com  | tee -a $INSTALLLOG
+#sudo gem install dm-core  | tee -a $INSTALLLOG
+#sudo gem install cehoffman-sinatra-respond_to -s http://gems.github.com  | tee -a $INSTALLLOG
+#sudo gem install rest-client | tee -a $INSTALLLOG
+#sudo gem install rack-contrib | tee -a $INSTALLLOG
+#sudo gem install thin | tee -a $INSTALLLOG
+#sudo gem install cucumber | tee -a $INSTALLLOG
+#sudo gem install datamapper | tee -a $INSTALLLOG
+#sudo gem install data_objects | tee -a $INSTALLLOG
+#sudo gem install do_sqlite3 | tee -a $INSTALLLOG
+#sudo gem install rinruby | tee -a $INSTALLLOG
+#sudo gem cleanup | tee -a $INSTALLLOG
+
+echo "Installing LibRDF-ruby"
+sudo apt-get install librdf0 librdf-ruby | tee -a $INSTALLLOG
+
+#GIT
+echo "Installing git from source"
+echo "This could take a while..."
+if [ ! -d $STARTPATH/git-$GITVERSION ];  
+then
+	wget http://www.kernel.org/pub/software/scm/git/git-$GITVERSION.tar.gz  >>$INSTALLLOG 2>>$ERRLOG
+	tar xzfv git-$GITVERSION.tar.gz  >>$INSTALLLOG 2>>$ERRLOG
+	cd git-$GITVERSION
+	./configure   >>$INSTALLLOG 2>>$ERRLOG
+	make   >>$INSTALLLOG 2>>$ERRLOG
+	sudo make install   >>$INSTALLLOG 2>>$ERRLOG
+	cd ..
+	sudo rm git-$GITVERSION.tar.gz
+	CHECKGIT=`git --version`
+	if [ "$CHECKGIT"  == "git version $GITVERSION" ]
+	then
+		echo "================================================="
+    		echo "Git version $GITVERSION successfully installed."
+		echo "================================================="
+	else
+	    echo "Git version $GITVERSION installation failed."
+	    FAILED=1
+	fi
+else
+	echo "git-$GITVERSION folder exists."
+fi
+
+#REDLAND
+if [ ! -d $STARTPATH/redland ];
+then
+	echo "Making Redland folder."
+	mkdir redland >>$INSTALLLOG 2>>$ERRLOG
+	cd redland
+	echo "Installing Redland raptor"
+	if [ ! -d $STARTPATH/redland/raptor-$RAPTORVERSION ];
+	then
+		wget wget http://download.librdf.org/source/raptor-$RAPTORVERSION.tar.gz  >>$INSTALLLOG 2>>$ERRLOG
+		tar xzfv raptor-$RAPTORVERSION.tar.gz  >>$INSTALLLOG 2>>$ERRLOG
+		cd raptor-$RAPTORVERSION
+		./configure  >>$INSTALLLOG 2>>$ERRLOG
+		sudo make   >>$INSTALLLOG 2>>$ERRLOG
+		sudo make install   >>$INSTALLLOG 2>>$ERRLOG
+		cd ..
+		sudo rm raptor-$RAPTORVERSION.tar.gz
+		CHECKRAPTOR=`raptor-config --version`
+		if [ "$CHECKRAPTOR"  == "$RAPTORVERSION" ]
+		then
+			echo "================================================="
+			echo "Raptor version $RAPTORVERSION successfully installed."
+			echo "================================================="
+		else
+		    echo "Raptor version $RAPTORVERSION installation failed."
+		    FAILED=1
+		fi
+	else
+		echo "raptor-$RAPTORVERSION folder exists."
+	fi
+
+	echo "Installing Redland rasqal"
+	wget wget http://download.librdf.org/source/rasqal-$RASQALVERSION.tar.gz  >>$INSTALLLOG 2>>$ERRLOG
+	tar xzfv rasqal-$RASQALVERSION.tar.gz  >>$INSTALLLOG 2>>$ERRLOG
+	cd rasqal-$RASQALVERSION
+	./configure  >>$INSTALLLOG 2>>$ERRLOG
+	sudo make   >>$INSTALLLOG 2>>$ERRLOG
+	sudo make install   >>$INSTALLLOG 2>>$ERRLOG
+	cd ..
+	sudo rm rasqal-$RASQALVERSION.tar.gz
+	CHECKRASQAL=`rasqal-config --version`
+	if [ "$CHECKRASQAL"  == "$RASQALVERSION2" -o  "$CHECKRASQAL"  == "$RASQALVERSION" ]
+	then
+		echo "================================================="
+		echo "Raptor version $RASQALVERSION2 or higher successfully installed."
+		echo "================================================="
+	else
+	    echo "Raptor version $RASQALVERSION2 or higher installation failed."
+	    FAILED=1
+	fi
+
+	echo "Installing Redland redland"
+	wget wget http://download.librdf.org/source/redland-$REDLANDVERSION.tar.gz  >>$INSTALLLOG 2>>$ERRLOG
+	tar xzfv redland-$REDLANDVERSION.tar.gz  >>$INSTALLLOG 2>>$ERRLOG
+	cd redland-$REDLANDVERSION
+	./configure  >>$INSTALLLOG 2>>$ERRLOG
+	sudo make   >>$INSTALLLOG 2>>$ERRLOG
+	sudo make install   >>$INSTALLLOG 2>>$ERRLOG
+	cd ..
+	sudo rm redland-$REDLANDVERSION.tar.gz
+	CHECKREDLAND=`redland-config --version`
+	if [ "$CHECKREDLAND"  == "$REDLANDVERSION" ]
+	then
+		echo "================================================="
+		echo "Redland version $REDLANDVERSION successfully installed."
+		echo "================================================="
+	else
+	    echo "Redland version $REDLANDVERSION installation failed."
+	    FAILED=1
+	fi
+
+
+	echo "Installing Redland Bindings with ruby"
+	wget http://download.librdf.org/source/redland-bindings-$REDBINDVERSION.tar.gz  >>$INSTALLLOG 2>>$ERRLOG
+	tar xzfv redland-bindings-$REDBINDVERSION.tar.gz  >>$INSTALLLOG 2>>$ERRLOG
+	cd redland-bindings-$REDBINDVERSION
+	./configure --with-ruby  >>$INSTALLLOG 2>>$ERRLOG
+	sudo make   >>$INSTALLLOG 2>>$ERRLOG
+	sudo make install   >>$INSTALLLOG 2>>$ERRLOG
+	cd ..
+	sudo rm redland-bindings-$REDBINDVERSION.tar.gz
+	cd ..
+	#CHECKREDBIND=`??? --version`
+	#if [ "$CHECKREDBIND"  == "$REDBINDVERSION" ]
+	#then
+	#	echo "================================================="
+	#	echo "Redland Bindings version $REDBINDVERSION successfully installed."
+	#	echo "================================================="
+	#else
+	#    echo "Redland Bindings version $REDBINDVERSION installation failed."
+	#    FAILED=1
+	#fi
+else
+	echo "Redland folder exists."
+fi
+
+echo "Installing the opentox webservices"
+mkdir webservices  
+cd webservices  
+
+echo "Install the opentox-ruby-api-wrapper"
+echo "This could take a while..."
+git clone git://github.com/helma/opentox-ruby-api-wrapper.git >>$INSTALLLOG 2>>$ERRLOG
+cd opentox-ruby-api-wrapper
+git checkout -b $BRANCH origin/$BRANCH >>$INSTALLLOG 2>>$ERRLOG
+OTAPIVERSION=`cat VERSION`
+sudo rake install  | tee -a $INSTALLLOG
+cd ..
+CHECKOTAPI=`gem list | grep "opentox-ruby-api-wrapper" | grep "$OTAPIVERSION"`
+if [ ! "$CHECKOTAPI" = '' ]
+then
+	echo "================================================="
+    	echo "opentox-ruby-api-wrapper ($OTAPIVERSION) successfully installed."
+	echo "================================================="
+else
+	echo "opentox-ruby-api-wrapper ($OTAPIVERSION) installation failed."
+	FAILED=1
+fi
+
+echo "Installing the webservices: compound, dataset, algorithm, model, task, feature"
+git clone git://github.com/helma/opentox-compound.git >>$INSTALLLOG 2>>$ERRLOG
+git clone git://github.com/helma/opentox-dataset.git >>$INSTALLLOG 2>>$ERRLOG
+# opentox-algorithem only temporally from davor!
+git clone git://github.com/davor/opentox-algorithm.git >>$INSTALLLOG 2>>$ERRLOG
+git clone git://github.com/helma/opentox-model.git >>$INSTALLLOG 2>>$ERRLOG
+git clone git://github.com/helma/opentox-task.git >>$INSTALLLOG 2>>$ERRLOG
+git clone git://github.com/helma/opentox-feature.git >>$INSTALLLOG 2>>$ERRLOG
+
+cd opentox-compound  
+git checkout -b $BRANCH origin/$BRANCH >>$INSTALLLOG 2>>$ERRLOG 
+cd ../opentox-dataset  
+git checkout -b $BRANCH origin/$BRANCH >>$INSTALLLOG 2>>$ERRLOG
+cd ../opentox-algorithm  
+git checkout -b $BRANCH origin/$BRANCH >>$INSTALLLOG 2>>$ERRLOG
+cd ../opentox-model  
+git checkout -b $BRANCH origin/$BRANCH >>$INSTALLLOG 2>>$ERRLOG
+cd ../opentox-task
+git checkout -b $BRANCH origin/$BRANCH >>$INSTALLLOG 2>>$ERRLOG
+cd ../opentox-task
+git checkout -b development origin/development >>$INSTALLLOG 2>>$ERRLOG
+cd ..  
+
+#edit /home/[username]/.opentox/config/test.yaml set :base_dir: /home/[username]/webservices
+
+echo "Installing the tests"                                                   
+git clone git://github.com/helma/opentox-test.git  >>$INSTALLLOG 2>>$ERRLOG   
+cd opentox-test                                                               
+git checkout -b $BRANCH origin/$BRANCH  >>$INSTALLLOG 2>>$ERRLOG       
+
+echo "Installing openbabel"
+cd ../opentox-compound
+sudo rake openbabel:install | tee -a $INSTALLLOG
+sudo ldconfig >>$INSTALLLOG 2>>$ERRLOG
+#VERSION=` --version`
+#if [ "$VERSION"  == "$RAPTORVERSION" ]
+#then
+#	echo "================================================="
+#    	echo "Raptor version $RAPTORVERSION successfully installed."
+#	echo "================================================="
+#else
+#    echo "Raptor version $RAPTORVERSION installation failed."
+#    FAILED=1
+#fi
+
+
+#check /webservices/opentox-algorithm/fminer.rb for 1,0/ture,false bug
+BUGCHECK1=`grep "@@fminer.AddActivity(true, id)" $STARTPATH/webservices/opentox-algorithm/fminer.rb`
+BUGCHECK2=`grep "@@fminer.AddActivity(false, id)" $STARTPATH/webservices/opentox-algorithm/fminer.rb`
+if [ -z "$BUGCHECK1$BUGCHECK2" ]
+then
+        echo "fminer.rb is correct."
+else
+        sed -i 's/@@fminer.AddActivity(true, id)/@@fminer.AddActivity(1, id)/g' $STARTPATH/webservices/opentox-algorithm/fminer.rb
+        sed -i 's/@@fminer.AddActivity(false, id)/@@fminer.AddActivity(0, id)/g' $STARTPATH/webservices/opentox-algorithm/fminer.rb
+        echo "fminer.rb updated."
+fi
+
+#todo: configure libfminer Makefile (location of ruby.h)
+#-> fixed by using davor's repository
+
+
+cd ../opentox-algorithm
+echo "Installing fminer"
+echo "This could take a while..."
+sudo updatedb
+sudo rake fminer:install | tee -a $INSTALLLOG
+cd ..
+FMINERVERSION=`ls $STARTPATH/webservices/opentox-algorithm/libfminer | grep "fminer.so"`
+if [ "$FMINERVERSION"  == "fminer.so" ]
+then
+	echo "================================================="
+    	echo "Fminer successfully installed."
+	echo "================================================="
+else
+    echo "Fminer installation failed."
+    FAILED=1
+fi
+
+if [ $FAILED == 0 ]
+then
+	#get username
+	echo "Please enter username:"
+	read USERNAME
+
+	#change rights from root to user
+	sudo chown -R $USERNAME: $STARTPATH/webservices/
+	sudo chown -R $USERNAME: ~/.opentox/
+fi
+
+if [ "$FAILED" == "1" ]
+then
+	echo "================================================="
+    	echo "Installation script failed!"
+	echo "================================================="
+    	exit 1
+else
+echo "================================================="
+echo "opentox-install-script is completed."
+echo "================================================="
+echo "Configuration:"
+echo "Edit the settings in $HOME/.opentox/config/{development|production|test}.yaml for your environment."
+echo "================================================="
+echo "Start the webservices local:"
+echo "cd webservices/opentox-test/"
+echo "rake opentox:services:start"
+echo "================================================="
+echo "Test local webservices:"
+echo "rake features"
+echo "================================================="
+fi
+exit 0