initial import

14 files changed, 281 insertions, 0 deletions

diff --git a/README b/README
index e69de29..05b9324 100644
--- a/README
+++ b/README
@@ -0,0 +1,8 @@
+Installer for OpenTox IST/ALU Services
+
+Usage (currently for Debian only):
+
+  git clone http://github.com/helma/opentox-install.git
+  cd opentox-install
+  vi config
+  sh install
diff --git a/config b/config
new file mode 100644
index 0000000..20da21d
--- /dev/null
+++ b/config
@@ -0,0 +1,28 @@
+#!/bin/sh
+
+# Configuration options for OpenTox installations (sets shell variables for installation scripts)
+
+# Linux distribution (currently only debian)
+distribution=debian
+
+# Choose a root password for the MySQL database
+# Please insert the correct password if mysql-server is already installed
+mysql_root=opentox
+
+# Services to be installed
+# Options:
+# gem	Installs only the opentox-ruby gem (useful, if you want to use external services with the opentox-ruby DSL)
+# all	Installs all IST/ALU services (useful for local and server installations)
+install=all
+
+# Installation type
+# Options:
+# local   local installation
+# server  inter or intranet server
+#type=local
+type=server
+
+# Git branch of services
+# Options: master test development
+# "master" is the current stable version
+branch=master
diff --git a/debian.sh b/debian.sh
new file mode 100644
index 0000000..1e9d5a0
--- /dev/null
+++ b/debian.sh
@@ -0,0 +1,20 @@
+#!/bin/sh
+
+echo "Downloading and updating Debian packages"
+apt-get install lsb-release
+codename=`lsb_release -a|grep Codename|cut -f2`
+if ! grep "^deb.*debian\.org.*non-free" /etc/apt/sources.list
+then
+  echo "deb http://ftp.debian.org/debian/ $codename non-free" | tee -a /etc/apt/sources.list
+fi
+apt-get update -y
+apt-get upgrade -y
+apt-get install binutils gcc g++ gfortran sun-java6-jdk -y
+apt-get install wget hostname pwgen git-core raptor-utils r-base -y # xvfb 
+. ./config
+echo mysql-server-5.1 mysql-server/root_password password $mysql_root | debconf-set-selections
+echo mysql-server-5.1 mysql-server/root_password_again password $mysql_root | debconf-set-selections
+apt-get install mysql-server -y
+apt-get install libssl-dev zlib1g-dev libreadline-dev libmysqlclient-dev libmysqlclient-dev libcurl4-openssl-dev libxml2-dev libxslt1-dev libgsl0.dev -y
+sed -i '/^JAVA_HOME=/d' /etc/profile
+echo 'export JAVA_HOME=/usr/lib/jvm/java-6-sun' | tee -a /etc/profile
diff --git a/install b/install
new file mode 100755
index 0000000..c29c514
--- /dev/null
+++ b/install
@@ -0,0 +1,17 @@
+#!/bin/sh
+
+. $distribution.sh
+. ruby.sh
+. nginx.sh
+. kernlab.sh
+. opentox-ruby.sh
+. ./config
+if [ $install = "all" ]
+then
+    . opentox-webservices.sh
+    . mysql-setup.sh
+    echo "Starting Nginx"
+    echo "Please inspect and tune /opt/nginx/conf/nginx.conf and /home/opentox/.opentox/config/production.yaml"
+    /opt/nginx/sbin/nginx
+fi
+
diff --git a/kernlab.sh b/kernlab.sh
new file mode 100644
index 0000000..d96e510
--- /dev/null
+++ b/kernlab.sh
@@ -0,0 +1,7 @@
+#!/bin/sh
+
+echo "Installing kernlab"
+. /etc/profile
+cd /tmp
+wget http://cran.r-project.org/src/contrib/Archive/kernlab/kernlab_0.9-11.tar.gz
+R CMD INSTALL kernlab_0.9-11.tar.gz
diff --git a/mysql-setup.sh b/mysql-setup.sh
new file mode 100644
index 0000000..d467cfa
--- /dev/null
+++ b/mysql-setup.sh
@@ -0,0 +1,11 @@
+#!/bin/sh
+
+echo "Initializing MySql"
+. ./config
+mysql -u root -p$mysql_root << EOF
+  DROP DATABASE IF EXISTS $branch;
+  CREATE DATABASE production;
+  GRANT ALL PRIVILEGES ON production.* TO production@localhost IDENTIFIED BY "$password";
+  FLUSH PRIVILEGES;
+EOF
+
diff --git a/nginx.conf b/nginx.conf
new file mode 100644
index 0000000..add5f85
--- /dev/null
+++ b/nginx.conf
@@ -0,0 +1,39 @@
+worker_processes  10;
+
+events {
+    worker_connections  1024;
+}
+
+http {
+
+    server_names_hash_bucket_size  256;
+
+    passenger_root /opt/ruby-enterprise-1.8.7-2010.02/lib/ruby/gems/1.8/gems/PASSENGER;
+    passenger_ruby /opt/ruby-enterprise-1.8.7-2010.02/bin/ruby;
+    passenger_default_user opentox;
+    passenger_log_level 3;
+
+    include       mime.types;
+    default_type  application/octet-stream;
+
+    sendfile        on;
+    keepalive_timeout  65;
+
+    # webservices
+    server {
+      listen 80;
+      client_max_body_size 5000m;
+      server_name SERVERNAME;
+      root /var/www/;
+
+      passenger_enabled on;
+      passenger_base_uri /compound;
+      passenger_base_uri /dataset;
+      passenger_base_uri /algorithm;
+      passenger_base_uri /model;
+      passenger_base_uri /task;
+      passenger_base_uri /validation;
+      passenger_base_uri /toxcreate;
+    }
+
+}
diff --git a/nginx.sh b/nginx.sh
new file mode 100644
index 0000000..b41636f
--- /dev/null
+++ b/nginx.sh
@@ -0,0 +1,11 @@
+#!/bin/sh
+
+. /etc/profile
+passenger-install-nginx-module --auto-download --auto --prefix=/opt/nginx
+
+cd /opt/ruby-enterprise-1.8.7-2010.02/lib/ruby/gems/1.8/gems/
+passenger=`ls -d passenger*`;
+cd -
+servername=`hostname`.`dnsdomainname`
+echo $passenger
+sed -e "s/PASSENGER/$passenger/;s/SERVERNAME/$servername/" nginx.conf > /opt/nginx/conf/nginx.conf
diff --git a/openbabel.sh b/openbabel.sh
new file mode 100644
index 0000000..27fa394
--- /dev/null
+++ b/openbabel.sh
@@ -0,0 +1,13 @@
+#!/bin/sh
+
+echo "Installing OpenBabel libraries"
+. /etc/profile
+cd /tmp
+wget -O - "http://downloads.sourceforge.net/project/openbabel/openbabel/2.2.3/openbabel-2.2.3.tar.gz?use_mirror=kent" | tar zxv
+cd openbabel-2.2.3/
+./configure
+make install
+cd scripts/ruby/
+ruby extconf.rb --with-openbabel-include=/usr/local/include/openbabel-2.0
+make install
+ldconfig
diff --git a/opentox-ruby.sh b/opentox-ruby.sh
new file mode 100644
index 0000000..47a20a7
--- /dev/null
+++ b/opentox-ruby.sh
@@ -0,0 +1,40 @@
+#!/bin/sh
+
+echo "Installing opentox-ruby gem"
+. /etc/profile
+. ./config
+gem install opentox-ruby
+
+# create config file
+password=`pwgen 8 1`
+servername=`hostname`.`dnsdomainname`
+if [ $branch = "development" ]
+then
+    logger=":logger: backtrace"
+else
+    logger=""
+fi
+
+if [ $type = "server" ]
+then
+    aa="https:\/\/opensso.in-silico.ch"
+else
+    aa=nil
+fi
+
+mkdir -p $HOME/.opentox/config
+mkdir -p $HOME/.opentox/log
+sed -e "s/PASSWORD/$password/;s/SERVERNAME/$servername/;s/LOGGER/$logger/;s/AA/$aa/" production.yaml > $HOME/.opentox/config/production.yaml
+
+ checkout development version and link lib to opentox-ruby gem
+if [ $branch = "development" ]
+then
+    cd /var/www/opentox
+    git clone http://github.com/mguetlein/opentox-ruby.git 
+    cd opentox-ruby
+    git checkout -t origin/$branch
+    gem_lib=`gem which opentox-ruby`
+    gem_lib=`echo $gem_lib | sed 's/\/opentox-ruby.rb//'`
+    mv $gem_lib $gem_lib~
+    ln -s /var/www/opentox/opentox-ruby/lib $gem_lib
+fi
diff --git a/opentox-webservices.sh b/opentox-webservices.sh
new file mode 100644
index 0000000..d22e5f4
--- /dev/null
+++ b/opentox-webservices.sh
@@ -0,0 +1,29 @@
+#!/bin/sh
+
+echo "Installing OpenTox webservices"
+. ./config
+# Create opentox system user
+id opentox
+if [ $? -ne 0 ] 
+then
+   adduser --system opentox
+fi
+
+mkdir -p /var/www/opentox
+cd /var/www/opentox
+for s in compound dataset algorithm model toxcreate task; do
+    git clone git://github.com/helma/opentox-$s.git $s
+    cd $s
+    git checkout -t origin/$branch
+    mkdir -p public
+    ln -s /var/www/opentox/$s/public /var/www/$s
+    cd -
+done
+git clone http://github.com/mguetlein/opentox-validation.git validation
+cd validation
+git checkout -t origin/$branch
+cd -
+cd /var/www/opentox/algorithm
+rake fminer:install
+chown -R opentox /var/www/opentox
+cd -
diff --git a/optional.sh b/optional.sh
new file mode 100644
index 0000000..ca33d03
--- /dev/null
+++ b/optional.sh
@@ -0,0 +1,3 @@
+#!/bin/sh
+
+apt-get install screen vim
diff --git a/production.yaml b/production.yaml
new file mode 100644
index 0000000..354f903
--- /dev/null
+++ b/production.yaml
@@ -0,0 +1,42 @@
+:base_dir: /var/www/opentox/
+
+:database: 
+# sqlite3 is not recommended (councurrent write)
+  :adapter:  mysql
+  :database: production
+  :username: production
+  :password: PASSWORD
+  :host:     localhost
+
+:services:
+# make sure to enter a full uri (including training slash)
+  opentox-compound:      "http://SERVERNAME/compound/"
+  opentox-dataset:       "http://SERVERNAME/dataset/"
+  opentox-algorithm:     "http://SERVERNAME/algorithm/"
+  opentox-model:         "http://SERVERNAME/model/"
+  opentox-task:          "http://SERVERNAME/task/"
+  opentox-toxcreate:     "http://SERVERNAME/toxcreate/"
+  opentox-validation:    "http://SERVERNAME/validation/"
+
+:yaml_hosts:
+  - "localhost"
+  - "SERVERNAME"
+  - "webservices.in-silico.ch"
+  - "opentox.informatik.uni-freiburg.de"
+
+# Uncomment for verbose logging
+LOGGER
+# :logger: debug
+
+# OpenSSO Authorization
+# set ":server: nil" to disable A&A
+:authorization:
+  :server: AA
+  :free_request: #not controlled by A&A
+    - "GET"  
+  :authenticate_request: #only for authenticated user
+    - "POST"
+  :authorize_request:  #only for authenticated and authorizeduser
+    - "DELETE"
+    - "PUT"
+ 
diff --git a/ruby.sh b/ruby.sh
new file mode 100644
index 0000000..2518939
--- /dev/null
+++ b/ruby.sh
@@ -0,0 +1,13 @@
+#!/bin/sh
+
+echo "Installing Ruby Enterprise"
+cd /tmp
+wget -O - "http://rubyforge.org/frs/download.php/71096/ruby-enterprise-1.8.7-2010.02.tar.gz" | tar zxv
+ruby-enterprise-1.8.7-2010.02/installer  --dont-install-useful-gems --no-dev-docs --auto=/opt/ruby-enterprise-1.8.7-2010.02
+sed -i '/^PATH=.*ruby-enterprise/d' /etc/profile
+echo 'PATH=$PATH:/opt/ruby-enterprise-1.8.7-2010.02/bin' | tee -a /etc/profile
+. /etc/profile
+gem sources -a http://gemcutter.org 
+gem sources -r http://rubygems.org/
+echo "gem: --no-ri --no-rdoc" | tee -a ~/.gemrc
+gem install passenger