Replaced README file with README.md

README.md

@@ -0,0 +1,82 @@
+AZOrange is a customization for the open source software Orange. 
+
+Installation (Using Ubuntu Precise Pangolin 12.04):
+===============================================================================
+**1.** Install all available system updates
+
+**2.** Download the '.tar.gz' latest version of AZOrange from https://github.com/AZCompTox/AZOrange/tags 
+
+**3.** Extract the code from the downloaded file:
+
+       tar xfz TheDownloadedFileName
+**4.** Step into AZCompTox-AZOrange-XXXXXXX/install
+
+       cd AZCompTox-AZOrange-XXXXXXX/install
+
+**5.** Prepare the system with 3rd party dependencies (inside the <installDir>/AZOrange/install dir):
+
+       ./prepareUbuntu4AZO.sh
+
+**6.** Create/configure a setup.ini file from a template (inside the <installDir>/AZOrange/install dir):
+
+       cp setup.ini.ubuntu setup.ini
+
+**7.** Edit the setup.ini to configure the destination install dir:
+
+       installDir = YourDesiredInstallFullPath
+
+   * Configure other settings if needed accordingly to your system.
+   * If using Ubuntu 10.04-64bits, also make the following changes:
+
+   **a** Change python version:
+   > PYTHON_VER = 2.6
+
+   **b** disable ftm:
+   > ;ftm = http://wwwkramer.in.tum.de/projects/ftm.tar.gz,0.1
+
+**8.** Start the installation scripts (inside the <installDir>/AZOrange/install dir):
+
+       python install.py
+
+**9.** After successful installation, there will be 3 ways of starting AZOrange:
+    **a** Click in the orange Icon installed in the Desktop (available if the installer found a way of creating it)
+    **b** In a terminal window, at the installDir, run the AZOrange start script:
+
+        ./startAZOrange
+
+   **c** Manually change shell, load the correct environment and start the application:
+
+        tcsh
+        source <installDir>/templateProfile
+        azorange
+
+
+Testing AZOrange installation
+===============================================================================
+
+**1.** Start a tcsh shell:
+
+        tcsh
+**2.** Load the AZOrange environment:
+
+        source <installDir>/templateProfile
+
+**3.** Change to the tests directory:
+
+        cd $AZORANGEHOME/tests
+
+**4.** Start the tests:
+
+        ./runOpenTests.sh
+
+
+Docummentation
+===============================================================================
+Please refer to the paper:
+http://www.jcheminf.com/content/3/1/28
+
+There are some examples and documentation in:
+
+    <installDir>/doc
+
+That is it!