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Diffstat (limited to 'bin/opentox-install-ubuntu.sh')
| -rwxr-xr-x | bin/opentox-install-ubuntu.sh | 375 |
1 files changed, 0 insertions, 375 deletions
diff --git a/bin/opentox-install-ubuntu.sh b/bin/opentox-install-ubuntu.sh deleted file mode 100755 index ae4807d..0000000 --- a/bin/opentox-install-ubuntu.sh +++ /dev/null @@ -1,375 +0,0 @@ -#!/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 |