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

   1. change to /some/directory
   2. uncompress and untar the artemis_compiled.tar.gz file
      On UNIX the command is:   tar xzvf artemis_compiled.tar.gz 

This will create a "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
diana 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
      make
   3. Run Artemis:
      ./art
      or ACT:
      ./act
      
Makefile targets
================

make		- compile code  
make jar	- create Artemis (jar_build/artemis.jar) and ACT 
			  (jar_build/act.jar) jar files.
make dist	- create a tar ball of the Artemis/ACT distribution

Creating signed jar files for Artemis/ACT Java Web Start launch
===============================================================

Use 'make jar' to create jar_build/artemis.jar. See the following pages 
for a description of deploying and signing jar files:

http://java.sun.com/docs/books/tutorial/deployment/webstart/deploying.html
http://java.sun.com/docs/books/tutorial/deployment/jar/signing.html

Use the Java keytool to generate a keystore (e.g. artemisstore below) file:

keytool -genkey -alias signFiles -dname "CN=$NAME, \
        OU=$ORGU, O=$ORG, L=$LOC, S=$STATE, C=$CODE" \
        -keypass $KEYPASS -storepass $STOREPASS -keystore artemisstore  -validity $VALID

The following can be used to view the key store and list entry details:

keytool -list -v -keystore artemisstore

Then use the following to create a signed jar to use in the JNLP file:

jarsigner -keystore artemisstore -storepass $STOREPASS -keypass $KEYPASS \
           -signedjar sartemis.jar artemis.jar signFiles

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

cd test
RunAllUnitTests.sh