Merge branch 'patch/JAL-3700_JAL-3748_JAL-3763_for_2_11_1_3' into releases/Release_2_...

[jalview.git] / README

diff --git a/README b/README
index 742ea2a..8172066 100755 (executable)
--- a/README
+++ b/README
@@ -1,28 +1,47 @@
-Jalview Release 2.01\r
--------------------\r
-\r
-\r
-\r
-This is the complete source for Jalview 2.01. \r
-\r
-The source is available as a tar file and comes complete with the GNU General Public License. \r
-\r
-To build the application you will need a J2SDK 1.4+. \r
-\r
-An Ant build file (build.xml) is provided, you will need to install Apache Ant first. Run ant to build the application, use the target "makeApplet" to make the Applet.\r
-\r
-You can also use Borland JBuilder to build Jalview. A JBuilder project file (JalviewX.jpx, JalviewApplet.jpx) for both application and applet is provided.\r
-\r
-For more help, read the file doc/building.html\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
-Replace JALVIEW_HOME with the full path to Jalview Installation Directory.
-\r
-##################\r
-\r
+Jalview Readme
+--------------
+
+
+The source is available as a tar file and comes complete with the GNU General Public License. 
+
+To build the application you will need a J2SDK 1.7+. 
+
+An Ant build file (build.xml) is provided, you will need to install Apache Ant first. 
+Run ant to view usage which will display a list of useful build targets.
+
+Jalview is primarily developed with eclipse, and a .project file is provided to simplify importing the source into your own eclipse workspace. A NetBeans nbbuild.xml file is also provided for developing Jalview with NetBeans - but this is not officially supported.
+
+You may also be able to use Borland JBuilder to build Jalview. A JBuilder project file 
+(JalviewX.jpx, JalviewApplet.jpx) for both application and applet is provided, 
+but the library dependencies are almost certainly out of date. See the build.xml 
+for current dependencies.
+
+For more help, read the file doc/building.html
+
+
+##################
+
+To run application...
+[ NOTE: when using the -classpath option with the '*' wildcard, the argument must be quoted to avoid shell expansion of the wildcard,
+  ALSO, the wildcard MUST be as DIR/* and not DIR/*.jar etc or it will not be interpreted correctly ]
+
+on Windows use:
+  java -classpath "JALVIEW_HOME/lib/*;JALVIEW_HOME/jalview.jar" jalview.bin.Jalview
+and on MacOS or Linux:
+  java -classpath "JALVIEW_HOME/lib/*:JALVIEW_HOME/jalview.jar" jalview.bin.Jalview
+
+Replace JALVIEW_HOME with the full path to Jalview Installation Directory. If building from source:
+
+  java -classpath "JALVIEW_BUILD/dist/*" jalview.bin.Jalview
+
+
+##################
+
+
+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