From 1130cf2d6e254b6b16358244116a4837352cb5bd Mon Sep 17 00:00:00 2001
From: Andreas Maunz <andreas@maunz.de>
Date: Thu, 22 Mar 2012 15:24:09 +0100
Subject: Modular: Initial version for main installer

---
 base-install.sh | 20 +++++++++++++++++--
 config.sh       | 22 +++++++--------------
 openbabel.sh    | 38 +++++++------------------------------
 ruby.sh         | 59 ++++++++++++++++++++++++++-------------------------------
 4 files changed, 59 insertions(+), 80 deletions(-)

diff --git a/base-install.sh b/base-install.sh
index 73c9e37..e9e0860 100644
--- a/base-install.sh
+++ b/base-install.sh
@@ -16,6 +16,7 @@ fi
 
 # Utils
 APTITUDE="`which aptitude`"
+GIT="`which git`"
 APT_CACHE="`which apt-cache`"
 DPKG="`which dpkg`"
 
@@ -24,10 +25,15 @@ if [ ! -e "$APTITUDE" ]; then
   exit 1
 fi
 
+if [ ! -e "$GIT" ]; then
+  echo "Git missing. Install git first." 1>&2
+  exit 1
+fi
+
 touch $OT_UI_CONF
 
 # Pkgs
-packs="binutils build-essential git-core gnuplot hostname libcurl4-openssl-dev libgsl0-dev libreadline6-dev libreadline-dev libsqlite3-dev libssl-dev libxml2-dev libxslt1-dev lsb-release openjdk-6-jdk psmisc pwgen raptor-utils r-base r-base-core r-base-dev sqlite3 wget xsltproc zlib1g-dev"
+packs="binutils build-essential cmake gnuplot hostname libcurl4-openssl-dev libgsl0-dev libreadline6-dev libreadline-dev libsqlite3-dev libssl-dev libxml2-dev libxslt1-dev lsb-release openjdk-6-jdk psmisc pwgen raptor-utils r-base r-base-core r-base-dev sqlite3 udev wget xsltproc zlib1g-dev"
 
 echo
 echo "Base Packages:"
@@ -65,7 +71,6 @@ if [ -n "$pack_fail" ]; then
   sleep 5
 fi
 
-echo sun-java6-jdk shared/accepted-sun-dlj-v1-1 select true | sudo /usr/bin/debconf-set-selections
 echo
 if [ -n "$pack_arr" ]; then 
   echo "Installing missing packages:"
@@ -92,5 +97,16 @@ if [ ! -f $JAVA_CONF ]; then
   fi
 fi
 
+if [ ! -d ~/.rbenv ]; then
+  cmd="$GIT clone git://github.com/sstephenson/rbenv.git ~/.rbenv" && run_cmd "$cmd" "rbenv"
+else
+  echo "'rbenv' already installed. Leaving untouched."
+fi
+
+if ! grep "rbenv" $OT_UI_CONF >/dev/null 2>&1 ; then
+  echo 'export PATH="$HOME/.rbenv/bin:$PATH"' >> $OT_UI_CONF
+  echo 'eval "$(rbenv init -)"' >> $OT_UI_CONF
+fi
+
 cd "$DIR"
 
diff --git a/config.sh b/config.sh
index 87b19b7..5bf084c 100755
--- a/config.sh
+++ b/config.sh
@@ -14,38 +14,30 @@ OT_PREFIX="$HOME/opentox-ruby"
 OT_JAVA_HOME="/usr/lib/jvm/java-6-openjdk"
 
 # 3) What versions to install.
-RUBY_NUM_VER="1.8.7-2011.03"
-OB_NUM_VER="2.2.3"
-KL_NUM_VER="0.9-11"
-REDIS_NUM_VER="2.4.4"
+RUBY_NUM_VER="1.9.3-p125"
+OB_NUM_VER="2.3.1"
+REDIS_NUM_VER="2.2.2"
 
 # 4) Server settings.
 NGINX_SERVERNAME="toxcreate3.in-silico.ch"
 WWW_DEST="$OT_PREFIX/www"
-NGINX_PORT="" # set to empty string ("") for port 80 otherwise set to port *using colon* e.g. ":8080"
-OHM_PORT="6379" # set to port (no colon)
+UNICORN_PORT="" # set to empty string ("") for port 80 otherwise set to port *using colon* e.g. ":8080"
+OHM_PORT="" # set to port (no colon)
 
 # Done.
 
 
 ### Nothing to gain from changes below this line.
 JAVA_CONF="$OT_PREFIX/.sh_java_ot"
-RUBY_CONF="$OT_PREFIX/.sh_ruby_ot"
-REDIS_CONF="$OT_PREFIX/.sh_redis_ot"
-NGINX_CONF="$OT_PREFIX/.sh_nginx_ot"
 OB_CONF="$OT_PREFIX/.sh_OB_ot"
-KL_CONF="$OT_PREFIX/.sh_R_ot"
+R_CONF="$OT_PREFIX/.sh_R_ot"
 
-RUBY_VER="ruby-enterprise-$RUBY_NUM_VER"
 OB_VER="openbabel-$OB_NUM_VER"
-KL_VER="$KL_NUM_VER"
 REDIS_VER="$REDIS_NUM_VER"
 
-RUBY_DEST="$OT_PREFIX/$RUBY_VER"
 OB_DEST="$OT_PREFIX/$OB_VER"
 OB_DEST_BINDINGS="$OT_PREFIX/openbabel-ruby-install"
-KL_DEST="$OT_PREFIX/r-packages"
-NGINX_DEST="$OT_PREFIX/nginx"
+R_DEST="$OT_PREFIX/r-packages"
 REDIS_DEST="$OT_PREFIX/redis-$REDIS_VER"
 
 REDIS_SERVER_CONF="$REDIS_DEST/redis.conf"
diff --git a/openbabel.sh b/openbabel.sh
index 3016d95..367fb28 100755
--- a/openbabel.sh
+++ b/openbabel.sh
@@ -19,6 +19,11 @@ if [ ! -e "$WGET" ]; then
   echo "'wget' missing. Install 'wget' first. Aborting..."
   exit 1
 fi
+CMAKE="`which cmake`"
+if [ ! -e "$CMAKE" ]; then
+  echo "'cmake' missing. Install 'cmake' first. Aborting..."
+  exit 1
+fi
 
 # Pkg
 LOG="$HOME/tmp/`basename $0`-log.txt"
@@ -45,9 +50,8 @@ if [ ! $OB_DONE ]; then
     cmd="tar zxf $OB_VER.tar.gz?use_mirror=kent $OB_VER"  && run_cmd "$cmd" "Unpack"
   fi
   cd "$HOME/tmp/$OB_VER">>$LOG 2>/dev/null
-
-  cmd="./configure --prefix=$OB_DEST" && run_cmd "$cmd" "Configure"
-  cmd="make" && run_cmd "$cmd" "Make"
+  cmd="$CMAKE -DCMAKE_INSTALL_PREFIX=$OB_DEST" && run_cmd "$cmd" "Configure"
+  cmd="make -j2" && run_cmd "$cmd" "Make"
   cmd="make install" && run_cmd "$cmd" "Install"
 fi
 
@@ -63,9 +67,6 @@ if [ ! -f "$OB_CONF" ]; then
   echo "if [ -z \"\$BABEL_DATADIR\" ]; then export BABEL_DATADIR=\"$OB_DEST/share/openbabel/$OB_NUM_VER\"; fi" >> "$OB_CONF"
   echo "if ! [ -d \"\$BABEL_DATADIR\" ]; then echo \"\$0: '\$BABEL_DATADIR' is not a directory!\"; fi" >> "$OB_CONF"
 
-  echo "if echo \"\$RUBYLIB\" | grep -v \"$OB_DEST_BINDINGS\">/dev/null 2>&1; then export RUBYLIB=\"$OB_DEST_BINDINGS:\$RUBYLIB\"; fi" >> "$RUBY_CONF"
-  echo "if ! [ -d \"$OB_DEST_BINDINGS\" ]; then echo \"\$0: '$OB_DEST_BINDINGS' is not a directory!\"; fi" >> "$RUBY_CONF"
-
   echo "Openbabel configuration has been stored in '$OB_CONF'."
   if ! grep "$OB_CONF" $OT_UI_CONF >/dev/null 2>&1 ; then
     echo ". \"$OB_CONF\"" >> $OT_UI_CONF
@@ -73,28 +74,3 @@ if [ ! -f "$OB_CONF" ]; then
 
 fi
 
-echo "Bindings:"
-OB_DONE=false
-. "$OT_UI_CONF"
-mkdir -p "$OB_DEST_BINDINGS">/dev/null 2>&1
-if [ ! -d "$OB_DEST_BINDINGS" ]; then
-  echo "Install directory '$OB_DEST_BINDINGS' is not available! Aborting..."
-  exit 1
-else
-  if [ "`ls $OB_DEST_BINDINGS | wc -l`" -gt 0 ]; then
-    OB_DONE=true
-  fi
-fi
-
-if ! $OB_DONE ; then
- OB_SRC_DIR="$HOME/tmp/$OB_VER/scripts/ruby/"
- cd "$OB_SRC_DIR"
- cmd="ruby extconf.rb --with-openbabel-include=$OB_DEST/include/openbabel-2.0 --with-openbabel-lib=$OB_DEST/lib" && run_cmd "$cmd" "Code"
- cmd="make" && run_cmd "$cmd" "Make"
- cmd="cp openbabel.so $OB_DEST_BINDINGS" && run_cmd "$cmd" "Install"
- cmd="ln -sf $OB_DEST_BINDINGS/openbabel.so $RUBY_DEST/lib/ruby/site_ruby/1.8/`uname -m`-linux/" && run_cmd "$cmd" "Link"
- cd "$DIR"
- . "`pwd`/utils.sh"
- cmd="ruby test-ob-rb.rb" && run_cmd "$cmd" "Load"
-fi
-
diff --git a/ruby.sh b/ruby.sh
index 2e53384..b88cfe2 100755
--- a/ruby.sh
+++ b/ruby.sh
@@ -19,12 +19,17 @@ if [ ! -e "$WGET" ]; then
   echo "'wget' missing. Install 'wget' first. Aborting..."
   exit 1
 fi
+RBENV="`which rbenv`"
+if [ ! -e "$RBENV" ]; then
+  echo "'rbenv' missing. Install 'rbenv' first. Aborting..."
+  exit 1
+fi
 
 # Pkg
 LOG="$HOME/tmp/`basename $0`-log.txt"
 
 echo
-echo "Ruby Enterprise edition ('$RUBY_DEST', '$LOG')."
+echo "Ruby ('$RUBY_DEST', '$LOG')."
 
 
 mkdir "$RUBY_DEST" >/dev/null 2>&1
@@ -39,45 +44,35 @@ fi
 
 if [ ! $RUBY_DONE ]; then
   cd $HOME/tmp
-  URI="http://rubyenterpriseedition.googlecode.com/files/$RUBY_VER.tar.gz"
-  if ! [ -d "$HOME/tmp/$RUBY_VER" ]; then
+  URI="http://ftp.ruby-lang.org/pub/ruby/1.9/$RUBY_VER.tar.gz"
+  if ! [ -d "$RUBY_VER" ]; then
     cmd="$WGET $URI" && run_cmd "$cmd" "Download"
     cmd="tar xzf $RUBY_VER.tar.gz" && run_cmd "$cmd" "Unpack"
   fi
-  cmd="sh $HOME/tmp/$RUBY_VER/installer  --dont-install-useful-gems --no-dev-docs --auto=$RUBY_DEST" && run_cmd "$cmd" "Install"
+  cmd="cd $RUBY_VER" && run_cmd "$cmd" "cd"
+  cmd="./configure --prefix=$RUBY_DEST" && run_cmd "$cmd" "Configure"
+  cmd="make" && run_cmd "$cmd" "Make"
+  cmd="make install" && run_cmd "$cmd" "Install"
+  cmd="cd -" && run_cmd "$cmd" "cd"
 fi
 
+cmd="$RBENV rehash" && run_cmd "$cmd" "Rbenv Update"
 
 
-if ! [ -f "$RUBY_CONF" ]; then
-  echo "if echo \"\$PATH\" | grep -v \"$RUBY_DEST\">/dev/null 2>&1; then export PATH=\"$RUBY_DEST/bin:\$PATH\"; fi" >> "$RUBY_CONF"
-
-  echo "Ruby configuration has been stored in '$RUBY_CONF'."
-  if ! grep "$RUBY_CONF" $OT_UI_CONF >/dev/null 2>&1 ; then
-    echo ". \"$RUBY_CONF\"" >> $OT_UI_CONF
-  fi
-fi
-. "$RUBY_CONF"
+#GEM="`which gem`"
+#if [ ! -e "$GEM" ]; then
+#  echo "'gem' missing. Install 'gem' first. Aborting..."
+#  exit 1
+#fi
+#
+#export PATH="$RUBY_DEST/bin:$PATH"
+#cmd="$GEM sources -a http://gemcutter.org" && run_cmd "$cmd" "Add Gemcutter"
+#cmd="$GEM sources -a http://rubygems.org" && run_cmd "$cmd" "Add Rubygems"
+#GEMCONF="gem: --no-ri --no-rdoc"
+#if ! grep "$GEMCONF" $HOME/.gemrc >>$LOG 2>&1; then
+#  echo "$GEMCONF" | tee -a $HOME/.gemrc >>$LOG 2>&1 
+#fi
 
 
-GEM="`which gem`"
-if [ ! -e "$GEM" ]; then
-  echo "'gem' missing. Install 'gem' first. Aborting..."
-  exit 1
-fi
-
-if [ "$PASSENGER_SKIP" != "s" ]; then
-  export PATH="$RUBY_DEST/bin:$PATH"
-  cmd="$GEM sources -a http://gemcutter.org" && run_cmd "$cmd" "Add Gemcutter"
-  cmd="$GEM sources -a http://rubygems.org" && run_cmd "$cmd" "Add Rubygems"
-  GEMCONF="gem: --no-ri --no-rdoc"
-  if ! grep "$GEMCONF" $HOME/.gemrc >>$LOG 2>&1; then
-    echo "$GEMCONF" | tee -a $HOME/.gemrc >>$LOG 2>&1 
-  fi
-  if ! $GEM list | grep passenger >/dev/null 2>&1; then
-    cmd="$GEM install passenger" && run_cmd "$cmd" "Install Passenger"
-  fi
   
-fi
-
 cd "$DIR"
-- 
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