Removed manual OB

4 files changed, 11 insertions, 91 deletions

diff --git a/base-install.sh b/base-install.sh
index 336126d..f6d8b4d 100755
--- a/base-install.sh
+++ b/base-install.sh
@@ -24,7 +24,7 @@ done
 touch "$OT_UI_CONF"
 
 # Pkgs
-packs="binutils build-essential cmake gnuplot hostname libcurl4-openssl-dev libgsl0-dev libreadline6-dev libreadline-dev libsqlite3-dev libssl-dev libyaml-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"
+packs="binutils build-essential cmake curl gnuplot hostname libcurl4-openssl-dev libgsl0-dev libopenbabel4 libopenbabel-dev libreadline6-dev libreadline-dev libsqlite3-dev libssl-dev libyaml-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:"
diff --git a/install b/install
index fa35845..1a3b7c3 100755
--- a/install
+++ b/install
@@ -8,15 +8,14 @@ if [ "$(id -u)" = "0" ]; then
 fi
 
 echo
-echo "Warning! Hit <Return> If all services are stoppped, else <Ctrl+C>."
-echo "Note: CONFIG (~/.opentox) will be backupped."
-read help_var
+echo "OpenTox Ruby"
+echo "Hit <Return> If all services are stoppped, else hit <Ctrl+C>."
+read delete_me
 
+echo "Note: CONFIG (~/.opentox) will be backupped."
 mkdir -p $OT_PREFIX/tmp/ >/dev/null 2>&1
 DATE=`date +_%Y%m%d_%H_%M`
-
-echo "Backups (if any)."
-echo
+echo "Backups (if any):"
 backup_targets="$HOME/.opentox $HOME/opentox-ruby"
 for bt in $backup_targets; do
   if [ -f $bt ]; then
@@ -25,29 +24,22 @@ for bt in $backup_targets; do
     mv -v --backup=numbered -T $bt $bt$DATE
   fi
 done
+echo "Backup finished."
 
 . ./utils.sh
-
-
 LOG="$OT_PREFIX/tmp/`basename $0`.log"
 echo
 echo "Welcome to base installation for OpenTox compatible services on Ruby and Debian."
-echo "This will install:"
-echo "- Debian packages"
-echo "- OpenBabel (from source)."
-echo
-echo "IMPORTANT: press Ctrl+C to adjust config.sh first (<Return> to continue)."
+echo "IMPORTANT: Hit <Ctrl+C> to adjust config.sh first (<Return> to continue)."
 read delete_me
 echo 
-echo "You may need to give root password for some privileged actions right now and later:"
-echo
-cmd="sudo echo -n \"\"" && run_cmd "$cmd" "Acquire privileges"
+echo -n "We need to install some packages. "
+sudo echo -n ""
 
 rm -rf $OT_PREFIX/tmp/openbabel* $OT_PREFIX/tmp/ruby*
 cmd="mkdir -p $OT_PREFIX/install && cp utils.sh $OT_PREFIX/install" && run_cmd "$cmd" "Install utils.sh to OT_PREFIX"
 cmd="mkdir -p $HOME/.opentox/config/install && cp config.sh $HOME/.opentox/config/install" && run_cmd "$cmd" "Install config.sh to CONFIG (~/.opentox)"
 . ./base-install.sh
-. ./openbabel.sh
 
 echo
 echo "Installation finished."
diff --git a/openbabel.sh b/openbabel.sh
deleted file mode 100755
index 93d606c..0000000
--- a/openbabel.sh
+++ /dev/null
@@ -1,55 +0,0 @@
-#!/bin/sh
-
-# Installs Openbabel.
-# Author: Christoph Helma, Andreas Maunz.
-# A configuration file is created and included in your 'OT_UI_CONF' (see config.sh).
-
-. ./utils.sh
-DIR=`pwd`
-OB_DWL="http://downloads.sourceforge.net/sourceforge/openbabel/$OB_NUM_VER/$OB_VER.tar.gz"
-
-[ "`id -u`" = "0" ] && echo "This script must be run as non-root." 1>&2 && exit 1
-
-# check utils
-utils="curl cmake"
-for u in $utils; do
-  eval `echo $u | tr "[:lower:]" "[:upper:]"`=`which $u` || (echo "'$u' missing. Install '$u' first." 1>&2 && exit 1)
-done
-
-# check openbabel
-LOG="$OT_PREFIX/tmp/`basename $0`.log"
-echo
-echo "Openbabel ('$OB_DEST', '$LOG'):"
-mkdir "$OB_DEST" >/dev/null 2>&1
-if [ ! -d "$OB_DEST" ]; then
-  echo "Install directory '$OB_DEST' is not available! Aborting..."
-  exit 1
-else
-  if ! rmdir "$OB_DEST" >/dev/null 2>&1; then # if not empty this will fail
-    OB_DONE=true
-  fi
-fi
-
-if [ ! $OB_DONE ]; then
-  cd "$OT_PREFIX/tmp">>$LOG 2>/dev/null
-  ([ -d "$OT_PREFIX/tmp/$OB_VER" ] || $CURL -L -d use_mirror=netcologne $OB_DWL 2>/dev/null | tar zx) && cd $OB_VER
-  cmd="$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
-
-if [ ! -f "$OB_CONF" ]; then
-  echo "if echo \"\$PATH\" | grep -v \"$OB_DEST\">/dev/null 2>&1; then export PATH=\"$OB_DEST/bin:\$PATH\"; fi" >> "$OB_CONF"
-  echo "if echo \"\$LD_LIBRARY_PATH\" | grep -v \"$OB_DEST\">/dev/null 2>&1; then export LD_LIBRARY_PATH=\"$OB_DEST/lib:\$LD_LIBRARY_PATH\"; fi" >> "$OB_CONF"
-  echo "if ! [ -d \"$OB_DEST\" ]; then echo \"\$0: '$OB_DEST' is not a directory!\"; fi" >> "$OB_CONF"
-  echo "if [ -z \"\$BABEL_LIBDIR\" ]; then export BABEL_LIBDIR=\"$OB_DEST/lib/openbabel/$OB_NUM_VER\"; fi" >> "$OB_CONF"
-  echo "if ! [ -d \"\$BABEL_LIBDIR\" ]; then echo \"\$0: '\$BABEL_LIBDIR' is not a directory!\"; fi" >> "$OB_CONF"
-  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 "Openbabel configuration has been stored in '$OB_CONF'."
-  if ! grep "$OB_CONF" $OT_UI_CONF >/dev/null 2>&1 ; then
-    echo ". \"$OB_CONF\"" >> $OT_UI_CONF
-  fi
-fi
-
-cd "$DIR"
diff --git a/utils.sh b/utils.sh
index 5cfec28..8b5bbd0 100755
--- a/utils.sh
+++ b/utils.sh
@@ -24,7 +24,7 @@ run_cmd ()
     tail -10 "$LOG"
     exit 1
   fi
-  printf "                              [ \033[32m%s\033[m ]\n" "OK"
+  printf "                              [  \033[32m%s\033[m  ]\n" "OK"
 }
 
 
@@ -52,23 +52,6 @@ install_ruby() {
 }
 
 
-install_ob_ruby() {
-  printf "\n%50s\n" "OB RUBY BINDINGS"
-  local DIR=`pwd`
-  check_utils "rbenv make"
-  SRC_DIR=$(dirname $(find $OT_PREFIX -name openbabel-ruby.cpp))
-  [ -d "$SRC_DIR" ] || (echo "Sources not found." 1>&2 && exit 1)
-  cd $SRC_DIR
-  cmd="$RBENV local $RUBY_NUM_VER" && run_cmd "$cmd" "Configure Ruby"
-  sed -i 's/Init_OpenBabel/Init_openbabel/g' openbabel-ruby.cpp # apply fix
-  cmd="ruby extconf.rb --with-openbabel-include=../../include --with-openbabel-lib=../../src/.libs" && run_cmd "$cmd" "Extconf ruby bindings"
-  cmd="$MAKE" && run_cmd "$cmd" "Make OB ruby bindings"
-  cmd="$MAKE install" && run_cmd "$cmd" "Install OB ruby bindings"
-  cd $DIR
-  cmd="$RBENV rehash" && run_cmd "$cmd" "Rbenv rehash"
-}
-
-
 install_with_bundler() {
   printf "\n%50s\n" "INSTALL"
   check_utils "gem rbenv"