additional instructions and use of -jar for launching

diff --git a/utils/InstallAnywhere/README_IA b/utils/InstallAnywhere/README_IA
index e317dbc..bb12463 100755 (executable)
--- a/utils/InstallAnywhere/README_IA
+++ b/utils/InstallAnywhere/README_IA
@@ -1,24 +1,31 @@
-Jalview Readme\r
---------------\r
-\r
-\r
-##################\r
-\r
-To run application:\r
-\r
-java -Djava.ext.dirs=JALVIEW_HOME/lib -cp JALVIEW_HOME/jalview.jar jalview.bin.Jalview\r
-\r
+Jalview Readme
+--------------
+
+
+##################
+
+To run application:
+
+java -Djava.ext.dirs=JALVIEW_HOME/lib -jar JALVIEW_HOME/jalview.jar [-help ... ]
+
 Replace JALVIEW_HOME with the full path to Jalview Installation Directory.
-\r
-##################\r
-\r
-\r
-\r
-\r
-If you use a proxy server add \r
-\r
--Dhttp.proxyServer=YOUR.SERVER -Dhttp.proxyPort=YOURPORT\r
-\r
-If the proxy server requires authentication, add\r
-\r
--Dhttp.proxyUser=USERNAME -Dhttp.proxyPassword=PASSWORD
\ No newline at end of file
+Use -help to see the available command line arguments.
+
+For best results use a Sun java run time environment (not the gcj gnu java, sorry!). 
+
+If you want to the java runtime bundled with Jalview, then launch jalview like this:
+
+JAVA_HOME=JALVIEW_HOME/jre JALVIEW_HOME/jre/bin/java -Djava.ext.dirs=JALVIEW_HOME/lib -jar JALVIEW_HOME/jalview.jar 
+
+Please Note: the -jar jalview.jar option launches the jalview.bin.Jalview class in the jalview.jar
+##################
+
+
+If you use a proxy server add 
+
+-Dhttp.proxyServer=YOUR.SERVER -Dhttp.proxyPort=YOURPORT
+
+If the proxy server requires authentication, add
+
+-Dhttp.proxyUser=USERNAME -Dhttp.proxyPassword=PASSWORD
+