Merge branch 'development' of git://github.com/opentox/install into development

2 files changed, 17 insertions, 6 deletions

diff --git a/README b/README
index 781a37c..8d86513 100644
--- a/README
+++ b/README
@@ -33,6 +33,7 @@ otconfig() {
 
 # Update the development version
 otupdate() {
+  START_DIR=`PWD`
   otconfig
   cd $HOME/opentox-ruby/www/opentox
   for d in `find -not -name "." -type d -maxdepth 1 2>/dev/null`; do echo $d ; cd $d ; git pull  ; echo ; cd - ;  done
@@ -41,7 +42,7 @@ otupdate() {
   mv liblast/Makefile liblast/Makefile~
   if ! git pull; then
     echo "Error! Pull for Fminer failed."
-    exit 1
+    return 1
   fi
   mv libbbrc/Makefile~ libbbrc/Makefile
   mv liblast/Makefile~ liblast/Makefile
@@ -53,12 +54,15 @@ otupdate() {
   cd $HOME/opentox-ruby/www/opentox/algorithm/last-utils
   if ! git pull; then
     echo "Error! Pull for Last-Utils failed."
-    exit 1
+    return 1
   fi
   cd -
   cd opentox-ruby
-  rake install
   LINK_DIR=`gem which opentox-ruby | sed 's/\/opentox-ruby.rb//'`
+  if [ -h $LINK_DIR ]; then 
+    rm -f $LINK_DIR
+  fi
+  rake install
   if ! [ -h $LINK_DIR ]; then
     echo "Warning! Your lib $LINK_DIR is no symlink. Linking back for you..."
     rm -rf "$LINK_DIR~"
@@ -66,6 +70,7 @@ otupdate() {
     ln -sf $HOME/opentox-ruby/www/opentox/opentox-ruby/lib `echo ${LINK_DIR::${#LINK_DIR}-4}`
   fi
   echo "Please execute 'otstart' to restart."
+  cd "START_DIR"
 }
 
 
@@ -94,6 +99,6 @@ otreload() {
 otkill() {
   sudo killall nginx >/dev/null 2>&1
   sudo bash -c "source $HOME/.opentox-ui.sh; redis-cli shutdown >/dev/null 2>&1"
-  while ps ax | grep PassengerHelperAgent | grep -v grep >/dev/null 2>&1; do sleep 1; done
+  while ps ax | grep PassengerWatchdog | grep -v grep >/dev/null 2>&1; do sleep 1; done
   for p in `pgrep R 2>/dev/null`; do sudo kill -9 $p; done
 }
diff --git a/opentox-webservices.sh b/opentox-webservices.sh
index 811d4bc..ef98ded 100755
--- a/opentox-webservices.sh
+++ b/opentox-webservices.sh
@@ -31,6 +31,12 @@ if [ ! -e "$GIT" ]; then
   exit 1
 fi
 
+RUBY="`which ruby`"
+if [ ! -e "$RUBY" ]; then
+  echo "'ruby' missing. Install 'ruby' first. Aborting..."
+  exit 1
+fi
+
 LOG="/tmp/`basename $0`-log.txt"
 
 echo
@@ -74,10 +80,10 @@ for mylib in bbrc last; do
 done
 cd "libfminer/libbbrc">>$LOG 2>&1
 cmd="make ruby" && run_cmd "$cmd" "Make BBRC"
-cd ->>$LOG 2>&1
+cd -
 cd "libfminer/liblast">>$LOG 2>&1
 cmd="make ruby" && run_cmd "$cmd" "Make LAST"
-cd ->>$LOG 2>&1
+cd -
 cd "last-utils">>$LOG 2>&1
 $GIT checkout $OT_BRANCH>>$LOG 2>&1
 $GIT pull >>$LOG 2>&1