solve merge conflicts with release/v2.1.0

1 files changed, 46 insertions, 0 deletions

diff --git a/README b/README
index 6746ce7..83ddf02 100644
--- a/README
+++ b/README
@@ -31,6 +31,49 @@ otconfig() {
   source $HOME/.opentox-ui.sh
 }
 
+# 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
+  cd  $HOME/opentox-ruby/www/opentox/algorithm/libfminer
+  mv libbbrc/Makefile libbbrc/Makefile~
+  mv liblast/Makefile liblast/Makefile~
+  if ! git pull; then
+    echo "Error! Pull for Fminer failed."
+    return 1
+  fi
+  mv libbbrc/Makefile~ libbbrc/Makefile
+  mv liblast/Makefile~ liblast/Makefile
+  make -C libbbrc/ clean
+  make -C libbbrc/ ruby
+  make -C liblast/ clean
+  make -C liblast/ ruby
+  cd -
+  cd $HOME/opentox-ruby/www/opentox/algorithm/last-utils
+  if ! git pull; then
+    echo "Error! Pull for Last-Utils failed."
+    return 1
+  fi
+  cd -
+  cd opentox-ruby
+  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~"
+    mv "$LINK_DIR" "$LINK_DIR~"
+    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"
+>>>>>>> release/v2.1.0
+}
+
 # Start the server
 otstart() {
   otkill
@@ -56,4 +99,7 @@ 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 PassengerWatchdog | grep -v grep >/dev/null 2>&1; do sleep 1; done
+  while ps ax | grep Rack | 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
 }