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

3 files changed, 14 insertions, 3 deletions

diff --git a/README b/README
index 2659a42..25aa733 100644
--- a/README
+++ b/README
@@ -36,14 +36,24 @@ otupdate() {
   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
+  git pull
+  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
+  git pull
+  cd -
   cd opentox-ruby
   rake install
   LINK_DIR=`gem which opentox-ruby | sed 's/\/opentox-ruby.rb//'`
   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~" >>$LOG 2>&1
-    ln -sf $HOME/opentox-ruby/www/opentox/opentox-ruby/lib $GEM_LIB
+    mv "$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."
 }
diff --git a/nginx.conf b/nginx.conf
index d3a8324..c89efe2 100644
--- a/nginx.conf
+++ b/nginx.conf
@@ -10,7 +10,7 @@ http {
 
     passenger_root RUBY_DEST/lib/ruby/gems/1.8/gems/PASSENGER;
     passenger_ruby RUBY_DEST/bin/ruby;
-    passenger_default_user opentox;
+    passenger_default_user USER;
     passenger_log_level 2;
     passenger_spawn_method conservative;
     #passenger_use_global_queue on;
diff --git a/nginx.sh b/nginx.sh
index 6b10a5c..800165e 100755
--- a/nginx.sh
+++ b/nginx.sh
@@ -52,6 +52,7 @@ cd - >>$LOG 2>&1
 servername=`hostname`
 $GIT checkout nginx.conf>>$LOG 2>&1
 cmd="sed -i -e \"s,PASSENGER,$passenger,;s,SERVERNAME,$servername,;s,RUBY_DEST,$RUBY_DEST,;s,NGINX_DEST,$NGINX_DEST,;s,WWW_DEST,$WWW_DEST,\" ./nginx.conf" && run_cmd "$cmd" "Config"
+cmd="sed -i -e \"s,USER,`whoami`,\" ./nginx.conf" && run_cmd "$cmd" "User"
 cmd="cp ./nginx.conf \"$NGINX_DEST/conf\"" && run_cmd "$cmd" "Copy"
 
 if [ ! -f $NGINX_CONF ]; then