Separate file for ot-tools

2 files changed, 85 insertions, 79 deletions

diff --git a/README b/README
index db3b9c0..00ed726 100644
--- a/README
+++ b/README
@@ -13,7 +13,11 @@ Here are some of my goals when writing the installer:
 - Encapsulated (everything is installed in a sub-directory in $HOME)
 - Logged (all non-elemtary actions are logged)
 
-Even if we officially support only *one* distro (currently Debian 6.0.1), I tested the installer successfully on various Ubuntus. In the README at the top are the requirements of the installer. By default, everything is installed to $HOME/opentox-ruby (=OT_PREFIX). The configs go to OT_PREFIX/.sh_<Package>_ot.sh for each package.
+
+Configure your system in config.sh. 
+NOTE for variable NGINX_PORT: leave this empty or set to ":80" to use port 80. If you do this, use the ot-scripts in "ot-tools-root.sh". Otherwise, if NGINX_PORT >1024, use ot-scripts in "ot-tools-user.sh".
+
+Even if we officially support only *one* distro (currently Debian 6.0.1), I tested the installer successfully on various Ubuntus. In this README at the top are the requirements of the installer. By default, everything is installed to $HOME/opentox-ruby (=OT_PREFIX). The configs go to OT_PREFIX/.sh_<Package>_ot.sh for each package.
 
 After running the installer, configure the system by editing the startup file of your favorite shell (in my case, BASH with the file ~ /. bashrc) to include ~/.opentox-ui.sh (in my case with 'source ...'). This file is the only one that the installer creates outside OT_PREFIX. Thus, the system is fully configured: If you now open a new shell, all environment variables will be adjusted.
 
@@ -24,82 +28,4 @@ nohup $HOME/opentox-ruby/nginx/sbin/nginx -c $HOME/opentox-ruby/nginx/conf/nginx
 To uninstall the system simply delete the link from the startup file: Done. To save disc space delete directory OT_PREFIX.
 Anyone can run multiple Opentox versions on the same machine: Just install again, but to a different OT_PREFIX. The switch works manually: Include the sh_<Package>_ot.sh files from the desired OT_PREFIX in $HOME/opentox-ui.sh (only one installation may be activated  at any time).
 
-Some useful scripts to put in your ~/.bashrc in case you are using bash (assuming OT_PREFIX is '~/opentox-ruby'):
-
-# Load server config
-otconfig() {
-  source $HOME/.opentox-ui.sh
-}
-
-# Update the 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 ; echo $d ; cd $d ; MYBRANCH=`git branch | grep "*" | sed 's/.*\ //g'`; git pull origin $MYBRANCH ; 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}-3}`
-  fi
-  echo "Please execute 'otstart' to restart."
-  cd "$START_DIR"
-}
-
-# Start the server
-otstart() {
-  otkill
-  bash -c "source $HOME/.opentox-ui.sh; nohup redis-server $HOME/opentox-ruby/redis-2.2.2/redis.conf >/dev/null 2>&1 &"
-  bash -c "source $HOME/.opentox-ui.sh; nohup nginx -c $HOME/opentox-ruby/nginx/conf/nginx.conf >/dev/null 2>&1 &"
-  sleep 2
-  if ! pgrep -u $USER nginx>/dev/null 2>&1; then echo "Failed to start nginx."; fi
-  if ! pgrep -u $USER redis-server>/dev/null 2>&1; then echo "Failed to start redis."; fi
-}
-
-# Display log
-alias otless='less $HOME/.opentox/log/production.log'
-
-# Tail log
-alias ottail='tail -f $HOME/.opentox/log/production.log'
-
-# Reload the server
-otreload() {
-  bash -c "source $HOME/.opentox-ui.sh; nginx -s reload"
-}
-
-# Kill the server
-otkill() {
-  killall nginx >/dev/null 2>&1
-  bash -c "source $HOME/.opentox-ui.sh; redis-cli shutdown >/dev/null 2>&1"
-  while ps x | grep PassengerWatchdog | grep -v grep >/dev/null 2>&1; do sleep 1; done
-  while ps x | grep Rack | grep -v grep >/dev/null 2>&1; do sleep 1; done
-  for p in `pgrep -u $USER R 2>/dev/null`; do kill -9 $p; done
-}
 
diff --git a/ot-tools-user.sh b/ot-tools-user.sh
new file mode 100644
index 0000000..64f26d3
--- /dev/null
+++ b/ot-tools-user.sh
@@ -0,0 +1,80 @@
+# Some useful scripts to put in your ~/.bashrc in case you are using bash (assuming OT_PREFIX is '~/opentox-ruby'):
+# USE ONLY IF YOUR NGINX PORT IS >1024 (NOT PRIVILEGED)
+
+# Load server config
+otconfig() {
+  source $HOME/.opentox-ui.sh
+}
+
+# Update the 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 ; echo $d ; cd $d ; MYBRANCH=`git branch | grep "*" | sed 's/.*\ //g'`; git pull origin $MYBRANCH ; 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}-3}`
+  fi
+  echo "Please execute 'otstart' to restart."
+  cd "$START_DIR"
+}
+
+# Start the server
+otstart() {
+  otkill
+  bash -c "source $HOME/.opentox-ui.sh; nohup redis-server $HOME/opentox-ruby/redis-2.2.2/redis.conf >/dev/null 2>&1 &"
+  bash -c "source $HOME/.opentox-ui.sh; nohup nginx -c $HOME/opentox-ruby/nginx/conf/nginx.conf >/dev/null 2>&1 &"
+  sleep 2
+  if ! pgrep -u $USER nginx>/dev/null 2>&1; then echo "Failed to start nginx."; fi
+  if ! pgrep -u $USER redis-server>/dev/null 2>&1; then echo "Failed to start redis."; fi
+}
+
+# Display log
+alias otless='less $HOME/.opentox/log/production.log'
+
+# Tail log
+alias ottail='tail -f $HOME/.opentox/log/production.log'
+
+# Reload the server
+otreload() {
+  bash -c "source $HOME/.opentox-ui.sh; nginx -s reload"
+}
+
+# Kill the server
+otkill() {
+  killall nginx >/dev/null 2>&1
+  bash -c "source $HOME/.opentox-ui.sh; redis-cli shutdown >/dev/null 2>&1"
+  while ps x | grep PassengerWatchdog | grep -v grep >/dev/null 2>&1; do sleep 1; done
+  while ps x | grep Rack | grep -v grep >/dev/null 2>&1; do sleep 1; done
+  for p in `pgrep -u $USER R 2>/dev/null`; do kill -9 $p; done
+}
+