POSIX compatible Installer for OpenTox IST/ALU Services
=======================================================

A) It is assumed that your system is configured for sudo to gain root privileges.
B) It is assumed that your system is configured for using non-free packages.

This is a POSIX-compliant  (not limited to a particular shell) Opentox installer. Please report bugs always via GitHub.

Here are some of my goals when writing the installer:
- Safe (existence of all the binaries will be checked before running, apart from GNU Core Utils)
- Idempotent (multiple execution does not change a thing)
- Atomic (return value of each non-elemtary action is asserted to be TRUE)
- 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.

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.

To start the system I run the following (but that is not part of the installer):
sudo nohup $HOME/opentox-ruby/redis-2.2.2/src/redis-server $HOME/opentox-ruby/redis-2.2.2/redis.conf &
sudo nohup $HOME/opentox-ruby/nginx/sbin/nginx -c $HOME/opentox-ruby/nginx/conf/nginx.conf &

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 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"
}

# Start the server
otstart() {
  otkill
  sudo bash -c "source $HOME/.opentox-ui.sh; nohup redis-server $HOME/opentox-ruby/redis-2.2.2/redis.conf >/dev/null 2>&1 &"
  sudo 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 nginx>/dev/null 2>&1; then echo "Failed to start nginx."; fi
  if ! pgrep 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() {
  sudo bash -c "source $HOME/.opentox-ui.sh; nginx -s reload"
}

# Kill the server
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
}