Installation instructions for UNIX
==================================

   1. change to /some/directory
   2. uncompress and untar the artemis-unix-releases-<version number>.tar.gz file
      On UNIX the command is:   tar xzvf artemis-unix-releases-<version number>.tar.gz

This will create an "artemis" directory containing all the java classes.  On
Unix the easiest way to run the program is to run the script called art in the
project directory:

    /some/directory/artemis/art

If all goes well you will be presented with a small window with two
menus.  From the File menu you can open a flat file containing an
entry.  If it reads the entry successfully a new window will open,
which shows the sequence and features for the entry.

Download and Install from GitHub
================================

Installation instructions for GitHub download

   1. Download:
      git clone http://github.com/sanger-pathogens/Artemis.git
   2. Compile the code:
      cd Artemis
      mvn clean package
   3. Run Artemis:
      ./art
      or ACT:
      ./act


Doing a full release with signed jar files
==========================================

You will need to drop the Pathogen Informatics Artemis maven.properties file in the project root, then run:

mvn -DEMBOSS_ROOT=<Emboss installation folder> clean release -P release

Running the test suite
======================

cd test

RunDefaultUnitTests.sh - this runs all non-automated unit tests.
RunEvoSuiteUnitTests.sh - this runs all EvoSuite generated unit tests. 
RunAllUnitTests.sh - this runs all non-automated and EvoSuite generated unit tests.