Reformat README to markdown

Makefile

@@ -72,7 +72,7 @@ manual :
 
 CLASS_FILES := `find org uk nsdb type seqdb -name '*.class' -print`
 
-OTHER_FILES := `find images/PSUlogo.gif images/icon.gif COPYING README`
+OTHER_FILES := `find images/PSUlogo.gif images/icon.gif COPYING README.md`
 
 dist :
 	rm -rf artemis_compiled.tar.gz tar_build
@@ -112,24 +112,24 @@ artemis.jar : $(CLASSES)
           done; \
         fi; \
 	cp -R ../lib/LICENSE.Apache ../uk ../org ../nsdb ../type ../seqdb ../etc ../images ../lib/j2ssh/j2ssh.properties \
-	      ../images/PSUlogo.gif ../images/icon.gif ../README ../artemis_sqlmap .
+	      ../images/PSUlogo.gif ../images/icon.gif ../README.md ../artemis_sqlmap .
 	find jar_build -name '*.java' -print | xargs rm -f
 	find jar_build -name '.svn' -print | xargs rm -rf
 	cd jar_build; \
 	rm -rf META-INF/MANIFEST.MF; \
 	echo "Main-Class: uk.ac.sanger.artemis.components.ArtemisMain\nPermissions: all-permissions" > manifest-art; \
-	jar cmf manifest-art artemis.jar META-INF/services images/PSUlogo.gif images/icon.gif README etc \
+	jar cmf manifest-art artemis.jar META-INF/services images/PSUlogo.gif images/icon.gif README.md etc \
 	                     artemis_sqlmap org uk com net nsdb type seqdb LICENSE.Apache j2ssh.properties; \
         echo "Main-Class: uk.ac.sanger.artemis.circular.DNADraw\nPermissions: all-permissions" > manifest-circular; \
-        jar cmf manifest-circular DNAPlotter.jar images/PSUlogo.gif README etc \
+        jar cmf manifest-circular DNAPlotter.jar images/PSUlogo.gif README.md etc \
                              uk org/gmod org/w3c org/apache org/biojava/bio/ com/ibatis/common/jdbc/ net/sf/samtools/ LICENSE.Apache j2ssh.properties; \
 	echo "Main-Class: uk.ac.sanger.artemis.components.alignment.BamView\nPermissions: all-permissions" > manifest-bamview; \
 	jar cmf manifest-bamview BamView.jar META-INF/services etc uk org/apache org/biojava org/biojavax org/gmod org/w3c net/sf com/ibatis; \
 	echo "Main-Class: uk.ac.sanger.artemis.components.ActMain\nPermissions: all-permissions" > manifest-act; \
-	jar cmf manifest-act act.jar META-INF/services images/PSUlogo.gif images/icon.gif README etc \
+	jar cmf manifest-act act.jar META-INF/services images/PSUlogo.gif images/icon.gif README.md etc \
 	                     artemis_sqlmap org uk com net nsdb type seqdb LICENSE.Apache j2ssh.properties; \
 	rm -f etc/log4j.properties; \
-	jar cmf manifest-art artemis_mac.jar images/PSUlogo.gif images/icon.gif README \
+	jar cmf manifest-art artemis_mac.jar images/PSUlogo.gif images/icon.gif README.md \
 	        uk org/gmod nsdb type seqdb LICENSE.Apache artemis_sqlmap
 
 clean :

README → README.md

-INTRODUCTION
+# INTRODUCTION
 
 [![Build Status](https://travis-ci.org/sanger-pathogens/Artemis.svg?branch=master)](https://travis-ci.org/sanger-pathogens/Artemis)
 
@@ -15,7 +15,7 @@ difference between genomes and to explore conservation of synteny, in the contex
 of the entire sequences and their annotation.
 
 
-DOCUMENTATION
+# DOCUMENTATION
 
 The Artemis user manual is at:
   http://www.sanger.ac.uk/resources/software/artemis/
@@ -23,12 +23,12 @@ The Artemis user manual is at:
 The ACT user manual is at:
   http://www.sanger.ac.uk/resources/software/act/
 
-INSTALLATION
+# INSTALLATION
 
 The installation instructions are included in the user manual.
 
 
-DISTRIBUTION
+# DISTRIBUTION
 
 Artemis may be freely distributed under the terms of the GNU Public License,
 and should run on any system with a recent version of Java.  
@@ -37,7 +37,7 @@ For information on how to get Artemis see this web page:
   http://www.sanger.ac.uk/resources/software/artemis/
 
 
-COPYRIGHT
+# COPYRIGHT
 
 Copyright (C) 1998-2013  Genome Research Limited