From 678a9e60be4a9a6b0c59969a0f6e0266885337fa Mon Sep 17 00:00:00 2001
From: gebele <gebele@in-silico.ch>
Date: Mon, 31 Oct 2016 16:09:18 +0000
Subject: updated README; added service commands for the gem

---
 README                  | 10 ----------
 README.md               | 52 +++++++++++++++++++++++++++++++++++++++++++++++++
 bin/nano-lazar-start    |  8 ++++++++
 bin/nano-lazar-start.sh |  8 ++++++++
 bin/nano-lazar-stop     |  5 +++++
 bin/nano-lazar-stop.sh  | 52 +++++++++++++++++++++++++++++++++++++++++++++++++
 nano-lazar.gemspec      | 12 ++++++++++--
 7 files changed, 135 insertions(+), 12 deletions(-)
 delete mode 100644 README
 create mode 100644 README.md
 create mode 100644 bin/nano-lazar-start
 create mode 100644 bin/nano-lazar-start.sh
 create mode 100644 bin/nano-lazar-stop
 create mode 100644 bin/nano-lazar-stop.sh

diff --git a/README b/README
deleted file mode 100644
index 12e0783..0000000
--- a/README
+++ /dev/null
@@ -1,10 +0,0 @@
-IST Software&Services
-
-Nano Lazar for eNanoMapper project
-
-installation:
-- bundle install
-
-usage:
--run 'unicorn -D'
--visit 'localhost:8080'
diff --git a/README.md b/README.md
new file mode 100644
index 0000000..ce3e52c
--- /dev/null
+++ b/README.md
@@ -0,0 +1,52 @@
+nano-lazar
+==========
+
+  nano-lazar for [eNanoMapper](http://www.enanomapper.net/) project.
+
+Dependencies
+------------
+
+  nano-lazar depends on a couple of external programs and libraries. All required libraries will be installed with the `gem install nano-lazar` or `bundle install` command. The output should give you more verbose information that can help in debugging (e.g. to identify missing libraries). 
+
+Installation
+------------  
+  
+  ```
+  gem install nano-lazar
+  ```
+
+  or
+
+  ```
+  git clone https://github.com/enanomapper/nano-lazar.git
+  cd nano-lazar
+  bundle install
+  ```
+
+Service
+-------
+
+  ```
+  nano-lazar-start
+  nano-lazar-stop
+  ```
+
+  or
+
+  ```
+  cd nano-lazar
+  unicorn -D
+  ```
+
+Browser
+-------
+  Point your browser to `localhost:8080` (default) or any other port passed within the unicorn start command.
+
+Documentation
+-------------
+  * [API documentation](http://rdoc.info/gems/nano-lazar)
+
+Copyright
+---------
+
+  Copyright (c) 2009-2016 Christoph Helma, Micha Rautenberg, Denis Gebele. See LICENSE for details.
diff --git a/bin/nano-lazar-start b/bin/nano-lazar-start
new file mode 100644
index 0000000..0cbaba5
--- /dev/null
+++ b/bin/nano-lazar-start
@@ -0,0 +1,8 @@
+#!/usr/bin/env ruby
+bin_dir = File.expand_path(File.dirname(__FILE__))
+shell_script_path = File.join(bin_dir, 'nano-lazar-start.sh')
+app_dir = File.expand_path('..')
+unicorn_conf = File.join(app_dir, 'unicorn.rb')
+
+`#{shell_script_path}`
+`#{unicorn_conf}`
diff --git a/bin/nano-lazar-start.sh b/bin/nano-lazar-start.sh
new file mode 100644
index 0000000..f772c66
--- /dev/null
+++ b/bin/nano-lazar-start.sh
@@ -0,0 +1,8 @@
+#!/bin/bash
+sudo mongod &
+R CMD Rserve
+GEMPATH=$(gem path nano-lazar)
+cd $GEMPATH
+unicorn -c unicorn.rb -E production -D
+
+exit 0
diff --git a/bin/nano-lazar-stop b/bin/nano-lazar-stop
new file mode 100644
index 0000000..b3ef727
--- /dev/null
+++ b/bin/nano-lazar-stop
@@ -0,0 +1,5 @@
+#!/usr/bin/env ruby
+bin_dir = File.expand_path(File.dirname(__FILE__))
+shell_script_path = File.join(bin_dir, 'nano-lazar-stop.sh')
+
+`#{shell_script_path}`
diff --git a/bin/nano-lazar-stop.sh b/bin/nano-lazar-stop.sh
new file mode 100644
index 0000000..ec91982
--- /dev/null
+++ b/bin/nano-lazar-stop.sh
@@ -0,0 +1,52 @@
+#!/bin/bash
+grep_nano_lazar=`ps aux | grep -v grep | grep nano-lazar-start`
+grep_mongo=`ps aux | grep -v grep | grep mongod`
+grep_rserve=`ps aux | grep -v grep | grep Rserve`
+grep_unicorn=`ps aux | grep -v grep | grep unicorn`
+
+# lazar
+if [ ${#grep_lazar} -gt 0 ]
+then
+  PID=`ps ax | grep -v grep | grep nano-lazar-start | awk '{ print $1 }'`
+  for i in "${PID}"
+  do
+    `kill $i`
+  done
+else
+  echo "nano-lazar is stopped."
+fi
+
+# mongod
+if [ ${#grep_mongo} -gt 0 ]
+then
+  PID=`ps ax | grep -v grep | grep mongod | awk '{ print $1 }'`
+  for i in "${PID}"
+  do 
+    `sudo kill $i`
+  done
+else
+  echo "MongoDB is not running."
+fi
+
+# rserve
+if [ ${#grep_rserve} -gt 0 ]
+then
+  PID=`ps ax | grep -v grep | grep Rserve | awk '{ print $1 }'`
+  for i in "${PID}"
+  do 
+    `kill $i`
+  done
+else
+  echo "Rserve is not running."
+fi
+
+# unicorn
+if [ ${#grep_unicorn} -gt 0 ]
+then
+  PID=`ps ax | grep -v grep | grep unicorn | awk '{ print $1 }'`
+  `kill ${PID[0]}`
+else
+  echo "Unicorn is not running."
+fi
+
+exit 0
diff --git a/nano-lazar.gemspec b/nano-lazar.gemspec
index 6e322f3..f3ec373 100644
--- a/nano-lazar.gemspec
+++ b/nano-lazar.gemspec
@@ -7,9 +7,9 @@ Gem::Specification.new do |s|
   s.email       = ["helma@in-silico.ch","rautenberg@in-silico.ch","gebele@in-silico.ch"]
   s.homepage    = "http://github.com/enanomapper/nano-lazar"
   s.summary     = %q{nano-lazar}
-  s.description = %q{Graphical User Interface for Nano Lazar Toxicology Predictions}
+  s.description = %q{Graphical user interface for nano-lazar toxicology predictions}
   s.license     = 'GPL-3'
-
+  s.executables = ["nano-lazar-start", "nano-lazar-stop"]
   s.rubyforge_project = "nano-lazar"
 
   s.files       = `git ls-files`.split("\n")
@@ -20,4 +20,12 @@ Gem::Specification.new do |s|
   s.add_runtime_dependency "rdiscount"
   s.add_runtime_dependency "haml"
   s.add_runtime_dependency "unicorn"
+  s.add_runtime_dependency "gem-path", "~> 0.6.1", '>= 0.6.1'
+
+  s.post_install_message = %q{
+    How to build nano-lazar prediction models described over here: https://github.com/opentox/lazar-public-data .  
+    Service commands:
+      nano-lazar-start
+      nano-lazar-stop
+  }
 end
-- 
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