add packagedir cli options to BEAST and BEAUti CompEvol/beast2#1070

CompEvol · Dec 14, 2022 · 87ec763 · 87ec763
1 parent c417ca1
commit 87ec763
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diff --git a/src/beastfx/app/beast/BeastMain.java b/src/beastfx/app/beast/BeastMain.java
@@ -159,6 +159,7 @@ public static void main(String[] args) {
                         new Arguments.StringOption("DFout", "DEFINITIONRESULTFILE", "BEAST XML file written when -DF option is used"),
                         new Arguments.Option("sampleFromPrior", "samples from prior for MCMC analysis (by adding sampleFromPrior=\"true\" in the first run element)"),
                         new Arguments.StringOption("version_file", "VERSIONFILE" ,"Provide a version file containing a list of services to explicitly allow. (Useful for package development.)").allowMultipleUse(),
+                        new Arguments.StringOption("packagedir", "PACKAGEDIR" ,"Set user package directory instead of using the default"),
                 });
 
         try {
@@ -171,6 +172,11 @@ public static void main(String[] args) {
             System.exit(1);
         }
 
+        if (arguments.hasOption("packagedir")) {
+            String dir = arguments.getStringOption("packagedir");
+            System.setProperty("beast.user.package.dir", dir);
+        }
+
         if (arguments.hasOption("loglevel")) {
             String l = arguments.getStringOption("loglevel");
             switch (l) {

diff --git a/src/beastfx/app/beauti/BeautiTabPane.java b/src/beastfx/app/beauti/BeautiTabPane.java
@@ -1241,6 +1241,13 @@ public void close() throws IOException {
 	        			i++;
 	        		}
 	        	}
+	        	if (args[i].equals("-packagedir")) {
+	        		args[i] = "";
+	        		i++;
+	                String dir = args[i];
+	                System.setProperty("beast.user.package.dir", dir);
+	        		args[i] = "";
+	            }
 	        }
 			if (Utils.isMac()) {
 			  	Utils.loadUIManager();