From d5e758fa924437e30dc65b80a46cafcf4691da2f Mon Sep 17 00:00:00 2001
From: Jim Procter <jprocter@issues.jalview.org>
Date: Wed, 5 Sep 2018 09:01:50 +0100
Subject: [PATCH] JAL-3065 - amended commit 
 4906697ab6e5a79fbce3baae89f7f64178c9a739  to exclude
 .settings/..groovy     Added notes to the instructions,
 also adjusted the jalviewDesktopRunner     test to lookup
 OS and use ';' or ':' accordingly.     All the
 CommandLineOperations tests failed on my (hastily set up)
 linux     box, so I'm committing and will test on MacOS
 too.

---
 README                                      |   11 ++++++++---
 src/jalview/bin/Jalview.java                |    8 +++++++-
 test/jalview/bin/CommandLineOperations.java |    8 +++++++-
 utils/InstallAnywhere/README_IA             |   12 +++++++++---
 4 files changed, 31 insertions(+), 8 deletions(-)

diff --git a/README b/README
index 74f4591..8172066 100755
--- a/README
+++ b/README
@@ -21,13 +21,18 @@ For more help, read the file doc/building.html
 
 ##################
 
-To run application:
+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 ]
 
-java -classpath "JALVIEW_HOME/lib/*:JALVIEW_HOME/jalview.jar" jalview.bin.Jalview
+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
+  java -classpath "JALVIEW_BUILD/dist/*" jalview.bin.Jalview
 
 
 ##################
diff --git a/src/jalview/bin/Jalview.java b/src/jalview/bin/Jalview.java
index 0b1cf60..adf3773 100755
--- a/src/jalview/bin/Jalview.java
+++ b/src/jalview/bin/Jalview.java
@@ -70,9 +70,15 @@ import groovy.util.GroovyScriptEngine;
 /**
  * Main class for Jalview Application <br>
  * <br>
- * start with java -classpath "$PATH_TO_LIB$/*:$PATH_TO_CLASSES$"
+ * start with: java -classpath "$PATH_TO_LIB$/*:$PATH_TO_CLASSES$" \
  * jalview.bin.Jalview
  * 
+ * or on Windows: java -classpath "$PATH_TO_LIB$/*;$PATH_TO_CLASSES$" \
+ * jalview.bin.Jalview jalview.bin.Jalview
+ * 
+ * (ensure -classpath arg is quoted to avoid shell expansion of '*' and do not
+ * embellish '*' to e.g. '*.jar')
+ * 
  * @author $author$
  * @version $Revision$
  */
diff --git a/test/jalview/bin/CommandLineOperations.java b/test/jalview/bin/CommandLineOperations.java
index 2b40a72..9b94be9 100644
--- a/test/jalview/bin/CommandLineOperations.java
+++ b/test/jalview/bin/CommandLineOperations.java
@@ -116,9 +116,15 @@ public class CommandLineOperations
   private Worker jalviewDesktopRunner(boolean withAwt, String cmd,
           int timeout)
   {
+    String cp_sep = ":";
+    if (System.getProperty("os.name").indexOf("Windows") >= 0)
+    {
+      cp_sep = ";";
+    }
     String _cmd = "java "
             + (withAwt ? "-Djava.awt.headless=true" : "")
-            + " -classpath \"./lib/*:./classes\" jalview.bin.Jalview ";
+            + " -classpath \"./lib/*" + cp_sep
+            + "./classes\" jalview.bin.Jalview ";
     System.out.println("CMD [" + cmd + "]");
     Process ls2_proc = null;
     Worker worker = null;
diff --git a/utils/InstallAnywhere/README_IA b/utils/InstallAnywhere/README_IA
index 3ccb2a4..82062f9 100755
--- a/utils/InstallAnywhere/README_IA
+++ b/utils/InstallAnywhere/README_IA
@@ -13,12 +13,18 @@ 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:
+If you want to use the java runtime bundled with Jalview, then launch jalview like this:
 
+in Windows:
+JAVA_HOME=JALVIEW_HOME/jre JALVIEW_HOME/jre/bin/java -classpath "JALVIEW_HOME/lib/*;JALVIEW_HOME/jalview.jar" jalview.bin.Jalview
+
+in Linux:
 JAVA_HOME=JALVIEW_HOME/jre JALVIEW_HOME/jre/bin/java -classpath "JALVIEW_HOME/lib/*:JALVIEW_HOME/jalview.jar" jalview.bin.Jalview
-[or
+
+in macOS:
 JAVA_HOME=JALVIEW_HOME/jre/Contents/Home JALVIEW_HOME/jre/Contents/Home/bin/java -classpath "JALVIEW_HOME/lib/*:JALVIEW_HOME/jalview.jar" jalview.bin.Jalview
-in macOS]
+
+Note: ensure the -classpath argument is quoted and only use a terminating wildcard (e.g. 'DIR/*') to refer to all jar files in a directory, don't use e.g. 'DIR/*.jar'
 
 ##################
 
-- 
1.7.10.2