X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=build.gradle;h=8efe39d8ddf813e74ca244518a3ffe196ccb460f;hb=2e57729baa0bc97fc03ab1fb8eb4dbc1a12f3d9a;hp=56140e6e3eb89f49d21a508419a60f07a49194a0;hpb=bec6abe894ca14c42017dfc8c30033e408a2d427;p=jalview.git

diff --git a/build.gradle b/build.gradle
index 56140e6..8efe39d 100644
--- a/build.gradle
+++ b/build.gradle
@@ -52,6 +52,7 @@ repositories {
 }
 
 
+
 // in ext the values are cast to Object. Ensure string values are cast as String (and not GStringImpl) for later use
 def string(Object o) {
   return o == null ? "" : o.toString()
@@ -1409,6 +1410,8 @@ jar {
   def outputDir = "${jalviewDir}/${package_dir}"
   destinationDirectory = file(outputDir)
   archiveFileName = rootProject.name+".jar"
+  duplicatesStrategy "EXCLUDE"
+
 
   exclude "cache*/**"
   exclude "*.jar"
@@ -1474,6 +1477,9 @@ shadowJar {
     attributes "Implementation-Version": JALVIEW_VERSION,
     "Application-Name": install4jApplicationName
   }
+
+  duplicatesStrategy "INCLUDE"
+
   mainClassName = shadow_jar_main_class
   mergeServiceFiles()
   classifier = "all-"+JALVIEW_VERSION+"-j"+JAVA_VERSION
@@ -2393,6 +2399,10 @@ task jalviewjsSyncAllLibs (type: Sync) {
   preserve {
     include "**"
   }
+
+  // should this be exclude really ?
+  duplicatesStrategy "INCLUDE"
+
   outputs.files outputFiles
   inputs.files inputFiles
 }
@@ -2640,7 +2650,7 @@ def jalviewjsCallCore(String name, FileCollection list, String prefixFile, Strin
           new org.apache.tools.ant.util.TeeOutputStream(
             logErrFOS,
             stderr),
-          errorOutput)
+          System.err)
     } else {
       standardOutput = new org.apache.tools.ant.util.TeeOutputStream(
         logOutFOS,
@@ -2949,8 +2959,8 @@ task jalviewjsServer {
 
     def factory
     try {
-      def class = Class.forName("SimpleHttpFileServerFactory")
-      factory = class.newInstance()
+      def f = Class.forName("org.gradle.plugins.javascript.envjs.http.simple.SimpleHttpFileServerFactory")
+      factory = f.newInstance()
     } catch (ClassNotFoundException e) {
       throw new GradleException("Unable to create SimpleHttpFileServerFactory")
     }