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|
#!/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
exit $FAILED
fi
else
echo "rubygems-$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
sudo apt-get install postgresql-server-dev-8.4 | 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 sinatra-respond_to | 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
exit $FAILED
fi
else
echo "git-$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
exit $FAILED
fi
else
echo "raptor-$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
exit $FAILED
fi
echo "Installing Redland redland"
wget wget http://download.librdf.org/source/redland-$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
exit $FAILED
fi
echo "Installing Redland Bindings with ruby"
wget http://download.librdf.org/source/redland-bindings-$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
# exit $FAILED
#fi
else
echo "Redland folder exists."
fi
echo "Installing the opentox webservices"
mkdir webservices
cd webservices
echo "Install the opentox-ruby-api-wrapper"
echo "This could take a while..."
git clone git://github.com/helma/opentox-ruby-api-wrapper.git >>$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
exit $FAILED
fi
echo "Installing the webservices: compound, dataset, algorithm, model, task, feature"
git clone git://github.com/helma/opentox-compound.git >>$INSTALLLOG 2>>$ERRLOG
git clone git://github.com/helma/opentox-dataset.git >>$INSTALLLOG 2>>$ERRLOG
git clone git://github.com/helma/opentox-algorithm.git >>$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
ln -s /usr/local/lib/libopenbabel.so.3 /usr/lib/libopenbabel.so.3 >> $INSTALLLOG 2>>$ERR
#VERSION=` --version`
#if [ "$VERSION" == "$RAPTORVERSION" ]
#then
# echo "================================================="
# echo "Raptor version $RAPTORVERSION successfully installed."
# echo "================================================="
#else
# echo "Raptor version $RAPTORVERSION installation failed."
# FAILED=1
# exit $FAILED
#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
exit $FAILED
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
|
