From a0aea2a33807f7c5072ebd1a672c7b537cee8312 Mon Sep 17 00:00:00 2001
From: davor <vorgrimmlerdavid@gmx.de>
Date: Mon, 8 Jul 2013 12:49:27 +0200
Subject: Removed system wide openbabel installation.

---
 base-install | 18 ++++++++++++------
 config.sh    |  2 +-
 install      |  4 ++--
 3 files changed, 15 insertions(+), 9 deletions(-)

diff --git a/base-install b/base-install
index 44abffd..326a908 100755
--- a/base-install
+++ b/base-install
@@ -23,8 +23,8 @@ echo "Updating index..."
 cmd="$WGET -O redland_key.asc $REDLAND_APT_KEY  >/dev/null 2>&1" && run_cmd "$cmd" "Download redland apt-key"
 cmd="$APT_KEY add redland_key.asc >/dev/null 2>&1; rm redland_key.asc" && run_cmd "$cmd" "Adding redland apt-key"
 if ! cat "/etc/apt/sources.list" | grep "$REDLAND_DEB">/dev/null 2>&1; then
-  echo "deb $REDLAND_DEB ./" | sudo $TEE -a /etc/apt/sources.list >/dev/null 
-  echo "deb-src $REDLAND_DEB ./" | sudo $TEE -a /etc/apt/sources.list >/dev/null 
+  echo "deb $REDLAND_DEB ./" | sudo $TEE -a /etc/apt/sources.list >/dev/null
+  echo "deb-src $REDLAND_DEB ./" | sudo $TEE -a /etc/apt/sources.list >/dev/null
 fi
 
 sudo $APTITUDE update -y >/dev/null 2>&1
@@ -39,16 +39,22 @@ case "$DISTRIB_INFO" in
 esac
 
 sudo $APTITUDE update -y >/dev/null 2>&1
+sudo $APT_GET install dselect
+sudo dselect update
 sudo $DPKG --set-selections < "$PACK_LIST"
 sudo $APT_GET -y --force-yes -u dselect-upgrade
 
 if [ ! -f $JAVA_CONF ]; then
 
   if [ ! -d "$OT_JAVA_HOME" ]; then
-    echo "Directory '$OT_JAVA_HOME' does not exist! Aborting..."
-    echo "Please check if openjdk-6-jdk has been installed properly."
-    echo "You may need to set the OT_JAVA_HOME variable in config.sh to the correct path on your system."
-    exit 1
+    if [ -d "$OT_JAVA_HOME-amd64" ]; then
+      OT_JAVA_HOME="$OT_JAVA_HOME-amd64"
+    else
+      echo "Directory '$OT_JAVA_HOME' does not exist! Aborting..."
+      echo "Please check if openjdk-6-jdk has been installed properly."
+      echo "You may need to set the OT_JAVA_HOME variable in config.sh to the correct path on your system."
+      exit 1
+    fi
   fi
 
   echo "if echo \"\$JAVA_HOME\" | grep -v \"$OT_JAVA_HOME\">/dev/null 2>&1; then export JAVA_HOME=\"$OT_JAVA_HOME\"; fi" >> "$JAVA_CONF"
diff --git a/config.sh b/config.sh
index 38e7772..4f48bb6 100755
--- a/config.sh
+++ b/config.sh
@@ -11,7 +11,7 @@ OT_BRANCH="development"     # Maturity              (development -need SSH key a
 
 # 2) Where binaries are installed
 OT_PREFIX="$HOME/opentox-ruby"
-OT_JAVA_HOME="/usr/lib/jvm/java-6-openjdk"
+OT_JAVA_HOME="/usr/lib/jvm/java-6-openjdk" # use "/usr/lib/jvm/java-6-openjdk-amd64" for 64bit system architecture
 
 # 3) What versions to install
 
diff --git a/install b/install
index 1dea679..cecf61d 100755
--- a/install
+++ b/install
@@ -45,7 +45,7 @@ if [ $SILENT = false ]; then
   read delete_me
 fi
 
-echo 
+echo
 echo -n "We need to do some privileged action. "
 sudo echo -n ""
 echo
@@ -55,7 +55,7 @@ echo
 [ -f $OT_DEFAULT_CONF ] || (cmd="echo '\$aa = { :uri => nil }' > $OT_DEFAULT_CONF" && run_cmd "$cmd" "default.rb => $HOME/.opentox/config")
 
 . ./base-install # Debian specific; disable this for others.
-./openbabel-install # Download, compile and build openbabel. Install to OT_PREFIX
+#./openbabel-install # Download, compile and build openbabel. Install to OT_PREFIX
 ./raptor2-install # Download, compile and build raptor2. Install to OT_PREFIX.
 ./rasqal-install # Download, compile and build rasqal. Install to OT_PREFIX.
 ./4store-install # Download, compile and build 4store. Install to OT_PREFIX.
-- 
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