mv TMP dir OT_PREFIX

4 files changed, 34 insertions, 33 deletions

diff --git a/base-install.sh b/base-install.sh
index e8bf173..fd50176 100755
--- a/base-install.sh
+++ b/base-install.sh
@@ -15,22 +15,23 @@ if [ "$(id -u)" = "0" ]; then
 fi
 
 # Utils
-APTITUDE="`which aptitude`"
-GIT="`which git`"
-APT_CACHE="`which apt-cache`"
-DPKG="`which dpkg`"
+APTITUDE=`which aptitude`
+GIT=`which git`
+APT_CACHE=`which apt-cache`
+DPKG=`which dpkg`
 
-if [ ! -e "$APTITUDE" ]; then
+if [ ! -e $APTITUDE ]; then
   echo "Aptitude missing. Install aptitude first." 1>&2
   exit 1
 fi
 
-if [ ! -e "$GIT" ]; then
+if [ ! -e $GIT ]; then
   echo "Git missing. Install git first." 1>&2
   exit 1
 fi
 
-touch $OT_UI_CONF
+# Init main file
+touch "$OT_UI_CONF"
 
 # Pkgs
 packs="binutils build-essential cmake gnuplot hostname libcurl4-openssl-dev libgsl0-dev libreadline6-dev libreadline-dev libsqlite3-dev libssl-dev 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"
@@ -40,16 +41,16 @@ echo "Base Packages:"
 
 echo
 echo "Updating index"
-sudo $APTITUDE update -y >/dev/null 2>&1
+sudo "$APTITUDE" update -y >/dev/null 2>&1
 
 echo
 echo "Checking installation:"
 pack_arr=""
 for p in $packs; do
-  if [ "un" != `$DPKG -l "$p" 2>/dev/null | tail -1 | awk -F " " '{print $1}'` ]; then
-     printf "%30s%50s\n" "'$p'" "Y"
+  if [ "un" != `$DPKG -l $p 2>/dev/null | tail -1 | awk -F " " '{print $1}'` ]; then
+     printf "%30s%50s\n" $p Y
   else
-     printf "%30s%50s\n" "'$p'" "N"
+     printf "%30s%50s\n" $p N
      pack_arr="$pack_arr $p"
   fi
 done
@@ -59,9 +60,9 @@ if [ -n "$pack_arr" ]; then
   echo "Checking availablity:"
   for p in $pack_arr; do
     if [ -n "`$APT_CACHE search $p`" ] ; then
-       printf "%30s%50s\n" "'$p'" "Y"
+       printf "%30s%50s\n" $p Y
     else
-      printf "%30s%50s\n" "'$p'" "N"
+      printf "%30s%50s\n" $p N
       pack_fail="$pack_fail $p"
     fi
   done
@@ -70,6 +71,7 @@ fi
 if [ -n "$pack_fail" ]; then
   echo 
   echo "WARNING: At least one missing package has no suitable installation candidate."
+  echo "$pack_fail"
   echo "Press <Ctrl+C> to abort (5 sec)."
   sleep 5
 fi
@@ -85,18 +87,18 @@ done
 
 if [ ! -f $JAVA_CONF ]; then
 
-  if [ ! -d "$OT_JAVA_HOME" ]; then
+  if [ ! -d $OT_JAVA_HOME ]; then
     echo "Directory '$OT_JAVA_HOME' does not exist! Aborting..."
     exit 1
   fi
 
-  echo "if echo \"\$JAVA_HOME\" | grep -v \"$OT_JAVA_HOME\">/dev/null 2>&1; then export JAVA_HOME=\"$OT_JAVA_HOME\"; fi" >> "$JAVA_CONF"
-  echo "if echo \"\$PATH\" | grep -v \"$OT_JAVA_HOME\">/dev/null 2>&1; then export PATH=\"$OT_JAVA_HOME:\$PATH\"; fi" >> "$JAVA_CONF"
-  echo "if ! [ -d \"\$JAVA_HOME\" ]; then echo \"\$0: '\$OT_JAVA_HOME' is not a directory!\"; fi" >> "$JAVA_CONF"
+  echo "if echo \$JAVA_HOME | grep -v \"$OT_JAVA_HOME\">/dev/null 2>&1; then export JAVA_HOME=\"$OT_JAVA_HOME\"; fi" >> "$JAVA_CONF"
+  echo "if echo \$PATH | grep -v \"$OT_JAVA_HOME\">/dev/null 2>&1; then export PATH=\"$OT_JAVA_HOME:\$PATH\"; fi" >> "$JAVA_CONF"
+  echo "if ! [ -d \$JAVA_HOME ]; then echo \"\$0: '\$OT_JAVA_HOME' is not a directory!\"; fi" >> "$JAVA_CONF"
 
   echo "Java configuration has been stored in '$JAVA_CONF'."
   if ! grep "$JAVA_CONF" $OT_UI_CONF >/dev/null 2>&1; then
-    echo ". \"$JAVA_CONF\"" >> $OT_UI_CONF
+    echo '. '$JAVA_CONF >> $OT_UI_CONF
   fi
 fi
 
diff --git a/install b/install
index 6ad23c3..1e4945b 100755
--- a/install
+++ b/install
@@ -13,7 +13,7 @@ echo "Note: Your data will be backupped."
 read help_var
 echo 
 
-mkdir -p $HOME/tmp/ >/dev/null 2>&1
+mkdir -p $OT_PREFIX/tmp/ >/dev/null 2>&1
 DATE=`date +_%Y%m%d_%H_%M`
 if [ -f "$HOME/.opentox-ui.sh" ]
 then
@@ -33,7 +33,7 @@ then
 else
   echo "$HOME/opentox-ruby not found (nothing to backup)."
 fi 
-LOG="$HOME/tmp/`basename $0`-log.txt"
+LOG="$OT_PREFIX/tmp/`basename $0`-log.txt"
 . "./utils.sh"
 echo
 echo "Opentox-ruby installation."
@@ -41,11 +41,11 @@ echo "You may need to give root password for some privileged actions right now a
 echo
 cmd="sudo echo -n \"\"" && run_cmd "$cmd" "Acquire privileges"
 
-echo "Cleaning up $HOME/tmp files."
-rm -rf $HOME/tmp/openbabel* $HOME/tmp/kernlab* $HOME/tmp/ruby*
+echo "Cleaning up $OT_PREFIX/tmp files."
+rm -rf $OT_PREFIX/tmp/openbabel* $OT_PREFIX/tmp/kernlab* $OT_PREFIX/tmp/ruby*
 
 . "./base-install.sh"
-#. "./openbabel.sh"
+. "./openbabel.sh"
 
 echo
 echo "Installation finished and system configured."
diff --git a/openbabel.sh b/openbabel.sh
index b51ed17..11656c9 100755
--- a/openbabel.sh
+++ b/openbabel.sh
@@ -26,7 +26,7 @@ if [ ! -e "$CMAKE" ]; then
 fi
 
 # Pkg
-LOG="$HOME/tmp/`basename $0`-log.txt"
+LOG="$OT_PREFIX/tmp/`basename $0`-log.txt"
 
 echo
 echo "Openbabel ('$OB_DEST', '$LOG'):"
@@ -43,13 +43,13 @@ else
 fi
 
 if [ ! $OB_DONE ]; then
-  cd "$HOME/tmp">>$LOG 2>/dev/null
+  cd "$OT_PREFIX/tmp">>$LOG 2>/dev/null
   URI="http://downloads.sourceforge.net/project/openbabel/openbabel/$OB_NUM_VER/$OB_VER.tar.gz?use_mirror=kent"
-  if ! [ -d "$HOME/tmp/$OB_VER" ]; then 
+  if ! [ -d "$OT_PREFIX/tmp/$OB_VER" ]; then 
     cmd="$WGET $URI" && run_cmd "$cmd" "Download"
     cmd="tar zxf $OB_VER.tar.gz?use_mirror=kent $OB_VER"  && run_cmd "$cmd" "Unpack"
   fi
-  cd "$HOME/tmp/$OB_VER">>$LOG 2>/dev/null
+  cd "$OT_PREFIX/tmp/$OB_VER">>$LOG 2>/dev/null
   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"
diff --git a/utils.sh b/utils.sh
index 880028c..0bc7801 100755
--- a/utils.sh
+++ b/utils.sh
@@ -2,11 +2,10 @@
 
 check_dest() 
 {
-  if ! [ -d "$OT_PREFIX" ]; then
-    if ! mkdir -p "$OT_PREFIX"; then
-      echo "Could not create target directory '$OT_PREFIX'! Aborting..."
-      exit 1
-    fi
+  [ -d "$OT_PREFIX/tmp" ] || mkdir -p "$OT_PREFIX/tmp"
+  if ! [ -d "$OT_PREFIX/tmp" ]; then
+    echo "Could not create target directory! Aborting..."
+    exit 1
   fi
 }
 
@@ -37,5 +36,5 @@ abs_path()
 
 . "`pwd`/config.sh"
 touch "$OT_UI_CONF"
-. "$OT_UI_CONF"
+. "$OT_UI_CONF" 2>/dev/null
 check_dest