From c796b25c1a70217a7f542bda4a7a51efb66f5b86 Mon Sep 17 00:00:00 2001
From: Christoph Helma <helma@in-silico.de>
Date: Tue, 17 Nov 2009 13:49:00 +0100
Subject: Passenger (re)start fixed

---
 bin/opentox-install-debian.sh | 105 ++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 105 insertions(+)
 create mode 100644 bin/opentox-install-debian.sh

(limited to 'bin')

diff --git a/bin/opentox-install-debian.sh b/bin/opentox-install-debian.sh
new file mode 100644
index 0000000..cf173da
--- /dev/null
+++ b/bin/opentox-install-debian.sh
@@ -0,0 +1,105 @@
+#!/bin/bash
+#Installation is tested on Debian Lenny Ubuntu 9.04
+#Update the system
+
+ERRLOG='install_err.log'
+INSTALLLOG='install_log.log'
+DATE=$(date +%Y/%m/%d\ %H:%M:%S)
+
+echo "================================================="
+echo "Please enshure that the sudo package is installed"
+echo "on your system. "
+echo "On Ubuntu Linux sudo is installed by default."
+echo "If you are unshure check with it 'sudo ls'"
+echo "and installed it with 'apt-get install sudo'"
+echo "and add your username with visudo."
+echo "================================================="
+echo -n "To continue installation press y: "
+read answer
+if [ "$answer" != "y" ]
+then
+  echo "exiting the script..."
+  exit 1
+fi
+
+echo "opentox webservice install log - " $DATE > $INSTALLLOG
+echo "Installing: build-essential"
+sudo apt-get install build-essential >> $INSTALLLOG 2>>$ERRLOG
+echo "Installing: ruby 1.8 with its dev files"
+sudo apt-get install ruby ruby1.8-dev >> $INSTALLLOG 2>>$ERRLOG
+echo "Installing: gems rdoc rubygems and rake"
+sudo apt-get install gems rdoc rubygems rake >> $INSTALLLOG 2>>$ERRLOG
+
+echo "Installing rubygems from source. This may take some time"
+wget http://rubyforge.org/frs/download.php/60718/rubygems-1.3.5.tgz >> $INSTALLLOG 2>>$ERRLOG
+tar xzfv rubygems-1.3.5.tgz 2>>$ERRLOG
+cd rubygems-1.3.5 >> $INSTALLLOG 2>>$ERRLOG
+sudo ruby setup.rb 2>>$ERRLOG
+cd ..
+
+echo "Adding http://gems.github.com to ruby gem sources"
+sudo gem sources -a http://gems.github.com >> $INSTALLLOG 2>>$ERRLOG
+
+#for debian lenny:
+echo "Installing packages: zlib1g-dev tcl curl perl ssh tcl tk8.5"
+sudo apt-get install zlib1g-dev tcl curl perl ssh tcl tk8.5  >> $INSTALLLOG 2>>$ERRLOG
+echo "Installing git from source"
+wget http://www.kernel.org/pub/software/scm/git/git-1.6.5.2.tar.gz >> $INSTALLLOG 2>>$ERRLOG
+tar xzfv git-1.6.5.2.tar.gz  2>>$ERRLOG
+cd git-1.6.5.2 >> $INSTALLLOG 2>>$ERRLOG
+./configure 2>>$ERRLOG
+make 2>>$ERRLOG
+make install 2>>$ERRLOG
+
+echo "Installing the opentox webservices"
+mkdir webservices >> $INSTALLLOG 2>>$ERRLOG
+cd webservices >> $INSTALLLOG 2>>$ERRLOG
+
+git clone git://github.com/helma/opentox-compound.git >> $INSTALLLOG 2>>$ERRLOG
+git clone git://github.com/helma/opentox-feature.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-test.git  >> $INSTALLLOG 2>>$ERRLOG
+
+cd opentox-compound >> $INSTALLLOG 2>>$ERRLOG
+git checkout -b development origin/development >> $INSTALLLOG 2>>$ERRLOG
+cd ../opentox-feature >> $INSTALLLOG 2>>$ERRLOG
+git checkout -b development origin/development >> $INSTALLLOG 2>>$ERRLOG
+cd ../opentox-dataset >> $INSTALLLOG 2>>$ERRLOG
+git checkout -b development origin/development >> $INSTALLLOG 2>>$ERRLOG
+cd ../opentox-algorithm >> $INSTALLLOG 2>>$ERRLOG
+git checkout -b development origin/development >> $INSTALLLOG 2>>$ERRLOG
+cd ../opentox-model >> $INSTALLLOG 2>>$ERRLOG
+git checkout -b development origin/development >> $INSTALLLOG 2>>$ERRLOG
+cd .. >> $INSTALLLOG 2>>$ERRLOG
+git clone git://github.com/helma/opentox-ruby-api-wrapper.git >> $INSTALLLOG 2>>$ERRLOG
+cd opentox-ruby-api-wrapper >> $INSTALLLOG 2>>$ERRLOG
+git checkout -b development origin/development >> $INSTALLLOG 2>>$ERRLOG
+rake install >> $INSTALLLOG 2>>$ERRLOG
+
+
+cd ../opentox-compound >> $INSTALLLOG 2>>$ERRLOG
+echo "Installing libopenssl-ruby"
+sudo apt-get install libopenssl-ruby >> $INSTALLLOG 2>>$ERRLOG
+echo "Installing dtach"
+rake dtach:install >> $INSTALLLOG 2>>$ERRLOG
+echo "Installing openbabel"
+rake openbabel:install >> $INSTALLLOG 2>>$ERRLOG
+
+#debian lenny missed liblink:
+ln -s /usr/local/lib/libopenbabel.so.3 /usr/lib/libopenbabel.so.3 >> $INSTALLLOG 2>>$ERRLOG
+
+rake redis:download >> $INSTALLLOG 2>>$ERRLOG
+rake redis:install >> $INSTALLLOG 2>>$ERRLOG
+#edit /home/[username]/.opentox/config/test.yaml set :base_dir: /home/[username]/webservices
+sudo apt-get install libgsl0-dev >> $INSTALLLOG 2>>$ERRLOG
+sudo apt-get install swig >> $INSTALLLOG 2>>$ERRLOG
+sudo apt-get install curl >> $INSTALLLOG 2>>$ERRLOG
+cd ../opentox-algorithm >> $INSTALLLOG 2>>$ERRLOG
+echo "Installing fminer"
+rake fminer:install >> $INSTALLLOG 2>>$ERRLOG
+sudo apt-get install libsqlite3-dev >> $INSTALLLOG 2>>$ERRLOG
+
+
+mkdir ../opentox-model/db >> $INSTALLLOG 2>>$ERRLOG
-- 
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