X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=build.gradle;h=23326433529b8e8309b6a7a87397806e9fecf288;hb=829eaee2c94fddaf65647191646b291d66f7ad0a;hp=ec8267ad048050d47d98c4ebbc7cadceeef30779;hpb=c6153fe9672b467fe579dfc4e8b7a827586d2d36;p=jalview.git

diff --git a/build.gradle b/build.gradle
index ec8267a..2332643 100644
--- a/build.gradle
+++ b/build.gradle
@@ -1,16 +1,22 @@
 import org.apache.tools.ant.filters.ReplaceTokens
+//import org.apache.tools.ant.filters.ReplaceRegexp
 import org.gradle.internal.os.OperatingSystem
+import org.gradle.plugins.ide.eclipse.model.*
 
 
+import groovy.transform.ExternalizeMethods
+
 buildscript {
   dependencies {
-    //classpath files("$gradlePluginsDir/gradle-macappbundle-2.3.0-patched-2.3.0.jar")
+    classpath 'org.openclover:clover:4.3.1'
+    classpath 'org.apache.commons:commons-compress:1.18'
   }
 }
 
 plugins {
   id 'java'
   id 'application'
+  id 'eclipse'
   id 'com.github.johnrengelman.shadow' version '4.0.3'
   id 'com.install4j.gradle' version '7.0.9'
 }
@@ -18,31 +24,232 @@ plugins {
 repositories {
   jcenter()
   mavenCentral()
+  mavenLocal()
   flatDir {
     dirs gradlePluginsDir
   }
 }
 
 mainClassName = launcherClass
+def cloverInstrDir = file("$buildDir/$cloverSourcesInstrDir")
+def classes = "$jalviewDir/$classesDir"
+
+if (clover.equals("true")) {
+  use_clover = true
+  classes = "$buildDir/$cloverClassesDir"
+} else {
+  use_clover = false
+  classes = "$jalviewDir/$classesDir"
+}
+
+// configure classpath/args for j8/j11 compilation
+
+def jalviewDirAbsolutePath = file(jalviewDir).getAbsolutePath()
+def libDir
+def libDistDir
+def compile_source_compatibility
+def compile_target_compatibility
+
+ext {
+  getdownWebsiteDir = jalviewDir + '/' + getdown_website_dir + '/' + JAVA_VERSION
+  getdownDir = ""
+  reportRsyncCmd = false
+  buildDist = true
+  buildProperties = buildPropertiesFile
+  switch (CHANNEL) {
+
+    case "BUILD":
+    // TODO: get bamboo build artifact URL for getdown artifacts
+    getdown_app_dir = getdown_app_dir_alt
+    buildProperties = jalviewDir + "/" + classesDir +"/" + buildPropertiesFile
+    break
+
+    case "RELEASE":
+    getdown_channel_name = CHANNEL.toLowerCase()
+    getdownDir = getdown_channel_name + "/" + JAVA_VERSION
+    getdown_app_base = getdown_channel_base + "/" + getdownDir
+    getdown_app_dir = getdown_app_dir_release
+    buildProperties = jalviewDir + "/" + classesDir +"/" + buildPropertiesFile
+    reportRsyncCommand = true
+    break
+
+    case "ARCHIVE":
+    getdown_channel_name = CHANNEL.toLowerCase()+"/"+JALVIEW_VERSION
+    getdownDir = getdown_channel_name + "/" + JAVA_VERSION
+    getdown_app_base = getdown_channel_base + "/" + getdownDir
+    getdown_app_dir = getdown_app_dir_alt
+    if (!file(ARCHIVEDIR+"/"+packageDir).exists()) {
+      print "Must provide an ARCHIVEDIR value to produce an archive distribution"
+      exit
+    } else {
+      packageDir = ARCHIVEDIR + "/" + packageDir
+      buildProperties = ARCHIVEDIR +"/" + classesDir + "/" + buildPropertiesFile
+      buildDist = false
+    }
+    reportRsyncCommand = true
+    break
+
+    case "ARCHIVELOCAL":
+    getdown_channel_name = "archive" + "/" + JALVIEW_VERSION
+    getdownDir = getdown_channel_name + "/" + JAVA_VERSION
+    getdown_app_base = file(getdownWebsiteDir).toURI().toString()
+    getdown_app_dir = getdown_app_dir_alt
+    if (!file(ARCHIVEDIR+"/"+packageDir).exists()) {
+      print "Must provide an ARCHIVEDIR value to produce an archive distribution"
+      exit
+    } else {
+      packageDir = ARCHIVEDIR + "/" + packageDir
+      buildProperties = ARCHIVEDIR +"/" + classesDir + "/" + buildPropertiesFile
+      buildDist = false
+    }
+    reportRsyncCommand = true
+    break
+
+    case "DEVELOP":
+    getdown_channel_name = CHANNEL.toLowerCase()
+    getdownDir = getdown_channel_name + "/" + JAVA_VERSION
+    getdown_app_base = getdown_channel_base + "/" + getdownDir
+    getdown_app_dir = getdown_app_dir_alt
+    buildProperties = jalviewDir + "/" + classesDir +"/" + buildPropertiesFile
+    reportRsyncCommand = true
+    break
+
+    case "TEST-RELEASE":
+    getdown_channel_name = CHANNEL.toLowerCase()
+    getdownDir = getdown_channel_name + "/" + JAVA_VERSION
+    getdown_app_base = getdown_channel_base + "/" + getdownDir
+    getdown_app_dir = getdown_app_dir_alt
+    buildProperties = jalviewDir + "/" + classesDir +"/" + buildPropertiesFile
+    reportRsyncCommand = true
+    break
+
+    case ~/^SCRATCH(|-[-\w]*)$/:
+    getdown_channel_name = CHANNEL
+    getdownDir = getdown_channel_name + "/" + JAVA_VERSION
+    getdown_app_base = getdown_channel_base + "/" + getdownDir
+    getdown_app_dir = getdown_app_dir_alt
+    buildProperties = jalviewDir + "/" + classesDir +"/" + buildPropertiesFile
+    reportRsyncCommand = true
+    break
+
+    case "LOCAL":
+    getdown_app_base = file(getdownWebsiteDir).toURI().toString()
+    getdown_app_dir = getdown_app_dir_alt
+    buildProperties = jalviewDir + "/" + classesDir +"/" + buildPropertiesFile
+    break
+
+    default: // something wrong specified
+    print("CHANNEL must be one of BUILD, RELEASE, ARCHIVE, DEVELOP, TEST-RELEASE, SCRATCH-..., LOCAL [default]")
+    exit
+    break
+
+  }
+
+  println("Using a "+CHANNEL+" profile. appbase="+getdown_app_base)
+  getdownAppDir = getdownWebsiteDir + '/' + getdown_app_dir
+  //getdownJ11libDir = getdownWebsiteDir + '/' + getdown_j11lib_dir
+  getdownResourceDir = getdownWebsiteDir + '/' + getdown_resource_dir
+  getdownInstallDir = getdownWebsiteDir + '/' + getdown_install_dir
+  getdownLauncher = jalviewDir + '/' + getdown_launcher
+  getdownFilesDir = jalviewDir + '/' + getdown_files_dir + '/' + JAVA_VERSION + '/'
+  getdownFilesInstallDir = getdownFilesDir+"/"+getdown_install_dir
+  /* compile without modules -- using classpath libraries
+  modules_compileClasspath = fileTree(dir: "$jalviewDir/$j11modDir", include: ["*.jar"])
+  modules_runtimeClasspath = modules_compileClasspath
+  */
+  gitHash = ""
+  gitBranch = ""
+}
+
+def JAVA_INTEGER_VERSION
+def additional_compiler_args = []
+// these are getdown.txt properties defined dependent on the JAVA_VERSION
+def getdown_alt_java_min_version
+def getdown_alt_java_max_version
+// this property is assigned below and expanded to multiple lines in the getdown task
+def getdown_alt_multi_java_location
+// this property is for the Java library used in eclipse
+def eclipse_java_runtime_name
+if (JAVA_VERSION.equals("1.8")) {
+  JAVA_INTEGER_VERSION = "8"
+  //libDir = j8libDir
+  libDir = j11libDir
+  libDistDir = j8libDir
+  compile_source_compatibility = 1.8
+  compile_target_compatibility = 1.8
+  getdown_alt_java_min_version = getdown_alt_java8_min_version
+  getdown_alt_java_max_version = getdown_alt_java8_max_version
+  getdown_alt_multi_java_location = getdown_alt_java8_txt_multi_java_location
+  eclipse_java_runtime_name = "JavaSE-1.8"
+} else if (JAVA_VERSION.equals("11")) {
+  JAVA_INTEGER_VERSION = "11"
+  libDir = j11libDir
+  libDistDir = j11libDir
+  compile_source_compatibility = 11
+  compile_target_compatibility = 11
+  getdown_alt_java_min_version = getdown_alt_java11_min_version
+  getdown_alt_java_max_version = getdown_alt_java11_max_version
+  getdown_alt_multi_java_location = getdown_alt_java11_txt_multi_java_location
+  eclipse_java_runtime_name = "JavaSE-11"
+  /* compile without modules -- using classpath libraries
+  additional_compiler_args += [
+  '--module-path', ext.modules_compileClasspath.asPath,
+  '--add-modules', j11modules
+  ]
+  */
+} else if (JAVA_VERSION.equals("12") || JAVA_VERSION.equals("13")) {
+  JAVA_INTEGER_VERSION = JAVA_VERSION
+  libDir = j11libDir
+  libDistDir = j11libDir
+  compile_source_compatibility = JAVA_VERSION
+  compile_target_compatibility = JAVA_VERSION
+  getdown_alt_java_min_version = getdown_alt_java11_min_version
+  getdown_alt_java_max_version = getdown_alt_java11_max_version
+  getdown_alt_multi_java_location = getdown_alt_java11_txt_multi_java_location
+  eclipse_java_runtime_name = "JavaSE-11"
+  /* compile without modules -- using classpath libraries
+  additional_compiler_args += [
+  '--module-path', ext.modules_compileClasspath.asPath,
+  '--add-modules', j11modules
+  ]
+  */
+} else {
+  throw new GradleException("JAVA_VERSION=$JAVA_VERSION not currently supported by Jalview")
+}
 
 sourceSets {
 
   main {
     java {
       srcDirs "$jalviewDir/$sourceDir"
-      outputDir = file("$jalviewDir/$classesDir")
+      outputDir = file("$classes")
     }
 
     resources {
       srcDirs "$jalviewDir/$resourceDir"
-      srcDirs "$jalviewDir/$libDir"
     }
 
     jar.destinationDir = file("$jalviewDir/$packageDir")
 
     compileClasspath = files(sourceSets.main.java.outputDir)
     compileClasspath += fileTree(dir: "$jalviewDir/$libDir", include: ["*.jar"])
-    //compileClasspath += fileTree(dir: "$jalviewDir/$j11libDir", include: ["*.jar"])
+
+    runtimeClasspath = compileClasspath
+  }
+  clover {
+    java {
+      srcDirs = [ cloverInstrDir ]
+      outputDir = file("${buildDir}/${cloverClassesDir}")
+    }
+
+    resources {
+      srcDirs = sourceSets.main.resources.srcDirs
+    }
+    compileClasspath = configurations.cloverRuntime + files( sourceSets.clover.java.outputDir )
+    compileClasspath += files(sourceSets.main.java.outputDir)
+    compileClasspath += sourceSets.main.compileClasspath
+    compileClasspath += fileTree(dir: "$jalviewDir/$utilsDir", include: ["**/*.jar"])
+    compileClasspath += fileTree(dir: "$jalviewDir/$libDir", include: ["*.jar"])
 
     runtimeClasspath = compileClasspath
   }
@@ -57,126 +264,403 @@ sourceSets {
       srcDirs = sourceSets.main.resources.srcDirs
     }
 
-    compileClasspath = sourceSets.main.compileClasspath
-    compileClasspath += files( sourceSets.test.java.outputDir )
+    compileClasspath = files( sourceSets.test.java.outputDir )
+
+    if (use_clover) {
+      compileClasspath += sourceSets.clover.compileClasspath
+    } else {
+      compileClasspath += files(sourceSets.main.java.outputDir)
+    }
+
     compileClasspath += fileTree(dir: "$jalviewDir/$utilsDir", include: ["**/*.jar"])
+    compileClasspath += fileTree(dir: "$jalviewDir/$libDir", include: ["*.jar"])
 
     runtimeClasspath = compileClasspath
   }
+}
 
-  modules {
-    compileClasspath = fileTree(dir: "$jalviewDir/$j11libDir", include: ["*.jar"])
+// clover bits
+dependencies {
+  if (use_clover) {
+    cloverCompile 'org.openclover:clover:4.3.1'
+    testCompile 'org.openclover:clover:4.3.1'
+  }
+}
 
-    runtimeClasspath = compileClasspath
+configurations {
+  cloverRuntime
+  cloverRuntime.extendsFrom cloverCompile
+}
+
+eclipse {
+  project {
+    name = "Jalview with gradle build"
+
+    natures 'org.eclipse.jdt.core.javanature',
+    'org.eclipse.jdt.groovy.core.groovyNature',
+    'org.eclipse.buildship.core.gradleprojectnature'
+
+    buildCommand 'org.eclipse.jdt.core.javabuilder'
+    buildCommand 'org.eclipse.buildship.core.gradleprojectbuilder'
+  }
+
+  classpath {
+    //defaultOutputDir = sourceSets.main.java.outputDir
+    def removeThese = []
+    configurations.each{ if (it.isCanBeResolved()) {
+      removeThese += it
+    }
+  }
+
+  minusConfigurations += removeThese
+  plusConfigurations = [ ]
+  file {
+
+    whenMerged { cp ->
+      def removeTheseToo = []
+      HashMap<String, Boolean> addedSrcPath = new HashMap<>();
+      cp.entries.each { entry ->
+        if (entry.kind == 'src') {
+          if (addedSrcPath.getAt(entry.path) || !(entry.path == "src" || entry.path == "test")) {
+            removeTheseToo += entry
+          } else {
+            addedSrcPath.putAt(entry.path, true)
+          }
+        }
+      }
+      cp.entries.removeAll(removeTheseToo)
+
+      print ("CP="+cp.inspect())
+
+      cp.entries += new Output("bin/main")
+      cp.entries += new Library(fileReference(helpParentDir))
+      cp.entries += new Library(fileReference(resourceDir))
+
+      HashMap<String, Boolean> addedLibPath = new HashMap<>();
+
+      // changing from sourcesets.main.classpath to specific Java version lib
+      //sourceSets.main.compileClasspath.each{
+      fileTree("$jalviewDir/$libDistDir").include("**/*.jar").include("*.jar").each {
+        //don't want to add outputDir as eclipse is using its own output dir in bin/main
+        if (it.isDirectory() || ! it.exists()) {
+          // don't add dirs to classpath
+          return
+        }
+        def itPath = it.toString()
+        if (itPath.startsWith(jalviewDirAbsolutePath+"/")) {
+          itPath = itPath.substring(jalviewDirAbsolutePath.length()+1)
+        }
+        if (addedLibPath.get(itPath)) {
+          //println("Not adding duplicate entry "+itPath)
+        } else {
+          //println("Adding entry "+itPath)
+          cp.entries += new Library(fileReference(itPath))
+          addedLibPath.put(itPath, true)
+        }
+      }
+
+      // changing from sourcesets.main.classpath to specific Java version lib
+      //sourceSets.test.compileClasspath.each{
+      fileTree(dir: "$jalviewDir/$utilsDir", include: ["**/*.jar"]).each {
+        //if ((it.isDirectory() || ! it.exists()) && ! (it.equals(sourceSets.main.java.outputDir))) {
+        //no longer want to add outputDir as eclipse is using its own output dir in bin/main
+        if (it.isDirectory() || ! it.exists()) {
+          // don't add dirs to classpath
+          return false // groovy "break" in .each loop
+        }
+        def itPath = it.toString()
+        if (itPath.startsWith(jalviewDirAbsolutePath+"/")) {
+          itPath = itPath.substring(jalviewDirAbsolutePath.length()+1)
+        }
+        if (addedLibPath.get(itPath)) {
+          // don't duplicate
+        } else {
+          def lib = new Library(fileReference(itPath))
+          // this doesn't work... yet.  Adding test=true attribute using withXml below
+          //def attrs = new Node(null, 'attributes', ["test":"true"])
+          //lib.appendNode(attrs) //
+          cp.entries += lib
+          addedLibPath.put(itPath, true)
+        }
+        }
+      }
+
+      // withXml changes ignored by buildship, these add the "test=true" attribute
+      withXml {
+        def node = it.asNode()
+
+        def srcTestAttributes
+        node.children().each{ cpe ->
+          def attributes = cpe.attributes()
+          if (attributes.get("kind") == "src" && attributes.get("path") == "test") {
+            srcTestAttributes = cpe.find { a -> a.name() == "attributes" }
+            return
+          }
+        }
+        def addTestAttribute = true
+        srcTestAttributes.each{a ->
+          if (a.name() == "attribute" && a.attributes().getAt("name") == "test") {
+            addTestAttribute = false
+          }
+        }
+        if (addTestAttribute) {
+          srcTestAttributes.append(new Node(null, "attribute", [name:"test", value:"true"]))
+        }
+
+        node.children().each{ cpe ->
+          def attributes = cpe.attributes()
+          if (attributes.get("kind") == "lib" && attributes.get("path").startsWith("utils/")) {
+            cpe.appendNode('attributes')
+            .appendNode('attribute', [name:"test", value:"true"])
+          }
+        }
+      } // withXML
+    } // file
+
+    containers 'org.eclipse.buildship.core.gradleclasspathcontainer'
+  } // classpath
+
+  jdt {
+    // for the IDE, use java 11 compatibility
+    sourceCompatibility = compile_source_compatibility
+    targetCompatibility = compile_target_compatibility
+    javaRuntimeName = eclipse_java_runtime_name
+
+    file {
+      withProperties { props ->
+        def jalview_prefs = new Properties()
+        def ins = new FileInputStream(jalviewDirAbsolutePath+"/"+eclipse_extra_jdt_prefs_file)
+        jalview_prefs.load(ins)
+        ins.close()
+        jalview_prefs.forEach { t, v ->
+          if (props.getAt(t) == null) {
+            props.putAt(t, v)
+          }
+        }
+      }
+    }
   }
 
+  //synchronizationTasks eclipseClasspath
+  //autoBuildTasks eclipseClasspath
 }
 
-compileJava {
+task cloverInstr() {
+  // only instrument source, we build test classes as normal
+  inputs.files files (sourceSets.main.allJava) // , fileTree(dir:"$jalviewDir/$testSourceDir", include: ["**/*.java"]))
+  outputs.dir cloverInstrDir
 
   doFirst {
-    if (JAVA_VERSION.equals("1.8")) {
-      sourceCompatibility = 1.8
-      targetCompatibility = 1.8
-    } else if (JAVA_VERSION.equals("11")) {
-      sourceCompatibility = 11
-      targetCompatibility = 11
-
-      options.compilerArgs = [
-        '--module-path', sourceSets.modules.compileClasspath.asPath,
-        '--add-modules', j11modules
-      ]
+    delete cloverInstrDir
+    def argsList = ["--initstring", "${buildDir}/clover/clover.db",
+    "-d", "${buildDir}/${cloverSourcesInstrDir}"]
+    argsList.addAll(inputs.files.files.collect({ file ->
+      file.absolutePath
+    }))
+    String[] args = argsList.toArray()
+    println("About to instrument "+args.length +" files")
+    com.atlassian.clover.CloverInstr.mainImpl(args)
+  }
+}
+
+
+task cloverReport {
+  group = "Verification"
+    description = "Createst the Clover report"
+    inputs.dir "${buildDir}/clover"
+    outputs.dir "${reportsDir}/clover"
+    onlyIf {
+      file("${buildDir}/clover/clover.db").exists()
     }
+  doFirst {
+    def argsList = ["--initstring", "${buildDir}/clover/clover.db",
+    "-o", "${reportsDir}/clover"]
+    String[] args = argsList.toArray()
+    com.atlassian.clover.reporters.html.HtmlReporter.runReport(args)
+
+    // and generate ${reportsDir}/clover/clover.xml
+    args = ["--initstring", "${buildDir}/clover/clover.db",
+    "-o", "${reportsDir}/clover/clover.xml"].toArray()
+    com.atlassian.clover.reporters.xml.XMLReporter.runReport(args)
+  }
+}
+
+// end clover bits
+
+
+compileJava {
+
+  doFirst {
+    sourceCompatibility = compile_source_compatibility
+    targetCompatibility = compile_target_compatibility
+    options.compilerArgs = additional_compiler_args
+    print ("Setting target compatibility to "+targetCompatibility+"\n")
   }
 
 }
 
+compileTestJava {
+  if (use_clover) {
+    dependsOn compileCloverJava
+    classpath += configurations.cloverRuntime
+  } else {
+    classpath += sourceSets.main.runtimeClasspath
+  }
+  doFirst {
+    sourceCompatibility = compile_source_compatibility
+    targetCompatibility = compile_target_compatibility
+    options.compilerArgs = additional_compiler_args
+    print ("Setting target compatibility to "+targetCompatibility+"\n")
+  }
+}
+
+
+compileCloverJava {
+
+  doFirst {
+    sourceCompatibility = compile_source_compatibility
+    targetCompatibility = compile_target_compatibility
+    options.compilerArgs += additional_compiler_args
+    print ("Setting target compatibility to "+targetCompatibility+"\n")
+  }
+  classpath += configurations.cloverRuntime
+}
+
 clean {
   delete sourceSets.main.java.outputDir
 }
 
 cleanTest {
   delete sourceSets.test.java.outputDir
+  delete cloverInstrDir
 }
 
+// format is a string like date.format("dd MMMM yyyy")
 def getDate(format) {
   def date = new Date()
-  //return date.format("dd MMMM yyyy")
   return date.format(format)
 }
 
-def getGitHash() {
-  def stdout = new ByteArrayOutputStream()
+task setGitVals {
+  def hashStdOut = new ByteArrayOutputStream()
   exec {
     commandLine "git", "rev-parse", "--short", "HEAD"
-    standardOutput = stdout
-    workingDir = jalviewDir
+    standardOutput = hashStdOut
+    ignoreExitValue true
   }
-  return stdout.toString().trim()
-}
 
-def getGitBranch() {
-  def stdout = new ByteArrayOutputStream()
+  def branchStdOut = new ByteArrayOutputStream()
   exec {
     commandLine "git", "rev-parse", "--abbrev-ref", "HEAD"
-    standardOutput = stdout
-    workingDir = jalviewDir
+    standardOutput = branchStdOut
+    ignoreExitValue true
   }
-  return stdout.toString().trim()
+
+  project.ext.gitHash = hashStdOut.toString().trim()
+  project.ext.gitBranch = branchStdOut.toString().trim()
+
+  outputs.upToDateWhen { false }
 }
 
 task createBuildProperties(type: WriteProperties) {
+  dependsOn setGitVals
   inputs.dir("$jalviewDir/$sourceDir")
+  inputs.dir("$classes")
   inputs.dir("$jalviewDir/$resourceDir")
-  outputFile "$jalviewDir/$classesDir/$buildPropertiesFile"
-  /* taking time/date specific comment out to allow better incremental builds */
-  //comment "--Jalview Build Details--\n"+getDate("yyyy-MM-dd HH:mm:ss")
-  comment "--Jalview Build Details--\n"+getDate("yyyy-MM-dd")
-  property "BUILD_DATE", getDate("dd MMMM yyyy")
+  outputFile (buildProperties)
+  // taking time specific comment out to allow better incremental builds
+  comment "--Jalview Build Details--\n"+getDate("yyyy-MM-dd HH:mm:ss")
+  //comment "--Jalview Build Details--\n"+getDate("yyyy-MM-dd")
+  property "BUILD_DATE", getDate("HH:mm:ss dd MMMM yyyy")
   property "VERSION", JALVIEW_VERSION
-  property "INSTALLATION", INSTALLATION+" git-commit:"+getGitHash()+" ["+getGitBranch()+"]"
+  property "INSTALLATION", INSTALLATION+" git-commit:"+project.ext.gitHash+" ["+project.ext.gitBranch+"]"
   outputs.file(outputFile)
-  outputs.dir("$jalviewDir/$classesDir")
+}
+
+def buildingHTML = "$jalviewDir/$docDir/building.html"
+task deleteBuildingHTML(type: Delete) {
+  delete buildingHTML
+}
+
+task convertBuildingMD(type: Exec) {
+  dependsOn deleteBuildingHTML
+  def buildingMD = "$jalviewDir/$docDir/building.md"
+  def css = "$jalviewDir/$docDir/github.css"
+
+  def pandoc = null
+  pandoc_exec.split(",").each {
+    if (file(it.trim()).exists()) {
+      pandoc = it.trim()
+      return true
+    }
+  }
+
+  def hostname = "hostname".execute().text.trim()
+  if ((pandoc == null || ! file(pandoc).exists()) && hostname.equals("jv-bamboo")) {
+    pandoc = System.getProperty("user.home")+"/buildtools/pandoc/bin/pandoc"
+  }
+
+  doFirst {
+    if (pandoc != null && file(pandoc).exists()) {
+        commandLine pandoc, '-s', '-o', buildingHTML, '--metadata', 'pagetitle="Building Jalview from Source"', '--toc', '-H', css, buildingMD
+    } else {
+        println("Cannot find pandoc. Skipping convert building.md to HTML")
+        throw new StopExecutionException()
+    }
+  }
+
+  ignoreExitValue true
+
+  inputs.file(buildingMD)
+  inputs.file(css)
+  outputs.file(buildingHTML)
+}
+clean {
+  delete buildingHTML
 }
 
 task syncDocs(type: Sync) {
-  def syncDir = "$jalviewDir/$classesDir/$docDir"
+  dependsOn convertBuildingMD
+  def syncDir = "$classes/$docDir"
   from fileTree("$jalviewDir/$docDir")
   into syncDir
 
 }
 
-def helpFile = "$jalviewDir/$classesDir/$helpDir/help.jhm"
-task syncHelp(type: Sync) {
-  inputs.files("$jalviewDir/$helpDir")
-  outputs.files(helpFile)
-
-  def syncDir = "$jalviewDir/$classesDir/$helpDir"
-  from fileTree("$jalviewDir/$helpDir")
-  into syncDir
-}
+def helpFile = "$classes/$helpDir/help.jhm"
 
 task copyHelp(type: Copy) {
-  def inputDir = "$jalviewDir/$helpDir"
-  def outputDir = "$jalviewDir/$classesDir/$helpDir"
-  from inputDir
+  def inputDir = "$jalviewDir/$helpParentDir/$helpDir"
+  def outputDir = "$classes/$helpDir"
+  from(inputDir) {
+    exclude '**/*.gif'
+      exclude '**/*.jpg'
+      exclude '**/*.png'
+      filter(ReplaceTokens, beginToken: '$$', endToken: '$$', tokens: ['Version-Rel': JALVIEW_VERSION])
+  }
+  from(inputDir) {
+    include '**/*.gif'
+      include '**/*.jpg'
+      include '**/*.png'
+  }
   into outputDir
-  filter(ReplaceTokens, beginToken: '$$', endToken: '$$', tokens: ['Version-Rel': "USING_FILTER"])
+
   inputs.dir(inputDir)
   outputs.files(helpFile)
   outputs.dir(outputDir)
 }
 
 task syncLib(type: Sync) {
-  def syncDir = "$jalviewDir/$classesDir/$libDir"
-  from fileTree("$jalviewDir/$libDir")
+  def syncDir = "$classes/$libDistDir"
+  from fileTree("$jalviewDir/$libDistDir")
   into syncDir
 }
 
 task syncResources(type: Sync) {
   from "$jalviewDir/$resourceDir"
   include "**/*.*"
-  into "$jalviewDir/$classesDir"
+  exclude "install4j"
+  into "$classes"
   preserve {
     include "**"
   }
@@ -188,28 +672,44 @@ task prepare {
   dependsOn copyHelp
 }
 
+
 //testReportDirName = "test-reports" // note that test workingDir will be $jalviewDir
 test {
   dependsOn prepare
   dependsOn compileJava
-  useTestNG {
+  if (use_clover) {
+    dependsOn cloverInstr
+  }
+
+  if (use_clover) {
+    print("Running tests " + (use_clover?"WITH":"WITHOUT") + " clover [clover="+use_clover+"]\n")
+  }
+
+  useTestNG() {
     includeGroups testngGroups
+    preserveOrder true
+    useDefaultListeners=true
   }
+
   workingDir = jalviewDir
   //systemProperties 'clover.jar' System.properties.clover.jar
+  sourceCompatibility = compile_source_compatibility
+  targetCompatibility = compile_target_compatibility
+  jvmArgs += additional_compiler_args
+  print ("Setting target compatibility to "+targetCompatibility+"\n")
 }
 
 task buildIndices(type: JavaExec) {
   dependsOn copyHelp
   classpath = sourceSets.main.compileClasspath
   main = "com.sun.java.help.search.Indexer"
-  workingDir = "$jalviewDir/$classesDir/$helpDir"
+  workingDir = "$classes/$helpDir"
   def argDir = "html"
   args = [ argDir ]
   inputs.dir("$workingDir/$argDir")
 
-  outputs.dir("$jalviewDir/$classesDir/doc")
-  outputs.dir("$jalviewDir/$classesDir/help")
+  outputs.dir("$classes/doc")
+  outputs.dir("$classes/help")
   outputs.file("$workingDir/JavaHelpSearch/DOCS")
   outputs.file("$workingDir/JavaHelpSearch/DOCS.TAB")
   outputs.file("$workingDir/JavaHelpSearch/OFFSETS")
@@ -224,24 +724,35 @@ task compileLinkCheck(type: JavaCompile) {
   destinationDir = file("$jalviewDir/$utilsDir")
   source = fileTree(dir: "$jalviewDir/$utilsDir", include: ["HelpLinksChecker.java", "BufferedLineReader.java"])
 
+  inputs.file("$jalviewDir/$utilsDir/HelpLinksChecker.java")
+  inputs.file("$jalviewDir/$utilsDir/HelpLinksChecker.java")
   outputs.file("$jalviewDir/$utilsDir/HelpLinksChecker.class")
   outputs.file("$jalviewDir/$utilsDir/BufferedLineReader.class")
 }
 
+def helplinkscheckertouchfile = file("$jalviewDir/$utilsDir/HelpLinksChecker.touch")
 task linkCheck(type: JavaExec) {
   dependsOn prepare, compileLinkCheck
   classpath = files("$jalviewDir/$utilsDir")
   main = "HelpLinksChecker"
-  workingDir = "$jalviewDir"
-  args = [ "$classesDir/$helpDir", "-nointernet" ]
+  workingDir = jalviewDir
+  def help = "$classes/$helpDir"
+  args = [ "$classes/$helpDir", "-nointernet" ]
 
-  doFirst {
-    standardOutput new FileOutputStream("$jalviewDir/$utilsDir/HelpLinksChecker.out")
+  doLast {
+    helplinkscheckertouchfile.createNewFile()
   }
 
-  outputs.file("$jalviewDir/$utilsDir/HelpLinksChecker.out")
+  inputs.dir("$classes/$helpDir")
+  outputs.file(helplinkscheckertouchfile)
 }
 
+// import the pubhtmlhelp target
+ant.properties.basedir = "$jalviewDir"
+ant.properties.helpBuildDir = jalviewDirAbsolutePath+"/$classes/$helpDir"
+ant.importBuild "$utilsDir/publishHelp.xml"
+
+
 task cleanPackageDir(type: Delete) {
   delete fileTree("$jalviewDir/$packageDir").include("*.jar")
 }
@@ -267,18 +778,18 @@ jar {
   exclude "**/*.jar"
   exclude "**/*.jar.*"
 
-  inputs.dir("$jalviewDir/$classesDir")
+  inputs.dir("$classes")
   outputs.file("$jalviewDir/$packageDir/$archiveName")
 }
 
 task copyJars(type: Copy) {
-  from fileTree("$jalviewDir/$classesDir").include("**/*.jar").include("*.jar").files
+  from fileTree("$classes").include("**/*.jar").include("*.jar").files
   into "$jalviewDir/$packageDir"
 }
 
 // doing a Sync instead of Copy as Copy doesn't deal with "outputs" very well
 task syncJars(type: Sync) {
-  from fileTree("$jalviewDir/$libDir").include("**/*.jar").include("*.jar").files
+  from fileTree("$jalviewDir/$libDistDir").include("**/*.jar").include("*.jar").files
   into "$jalviewDir/$packageDir"
   preserve {
     include jar.archiveName
@@ -286,6 +797,8 @@ task syncJars(type: Sync) {
 }
 
 task makeDist {
+  group = "build"
+  description = "Put all required libraries in dist"
   // order of "cleanPackageDir", "copyJars", "jar" important!
   jar.mustRunAfter cleanPackageDir
   syncJars.mustRunAfter cleanPackageDir
@@ -302,62 +815,88 @@ task cleanDist {
 }
 
 shadowJar {
-  dependsOn makeDist
-  if (JAVA_VERSION.equals("11")) {
-    from ("$jalviewDir/$j11libDir") {
-      include("*.jar")
-    }
+  group = "distribution"
+  if (buildDist) {
+    dependsOn makeDist
+  }
+  from ("$jalviewDir/$libDistDir") {
+    include("*.jar")
+  }
+  manifest {
+    attributes 'Implementation-Version': JALVIEW_VERSION
   }
   mainClassName = shadowJarMainClass
   mergeServiceFiles()
-  classifier = "all"
+  classifier = "all-"+JALVIEW_VERSION+"-j"+JAVA_VERSION
   minimize()
 }
 
-ext {
-  getdownWebsiteDir = jalviewDir + '/' + getdown_website_dir
-  getdownAppDir = getdownWebsiteDir + '/' + getdown_app_dir
-  getdownJ11libDir = getdownWebsiteDir + '/' + getdown_j11lib_dir
-  getdownResourceDir = getdownWebsiteDir + '/' + getdown_resource_dir
-  getdownLauncher = jalviewDir + '/' + getdown_launcher
-  getdownFilesDir = jalviewDir + '/' + getdown_files_dir
-}
-
 task getdownWebsite() {
-  dependsOn makeDist
+  group = "distribution"
+  description = "Create the getdown minimal app folder, and website folder for this version of jalview. Website folder also used for offline app installer"
+  if (buildDist) {
+    dependsOn makeDist
+  }
+
+	// clean the getdown website and files dir before creating getdown folders
+	delete project.ext.getdownWebsiteDir
+	delete project.ext.getdownFilesDir
+
   def getdownWebsiteResourceFilenames = []
   def getdownTextString = ""
   def getdownResourceDir = project.ext.getdownResourceDir
   def getdownAppDir = project.ext.getdownAppDir
   def getdownResourceFilenames = []
+
   doFirst {
+    copy {
+      from buildProperties
+      rename(buildPropertiesFile, getdown_build_properties)
+      into project.ext.getdownAppDir
+    }
+    getdownWebsiteResourceFilenames += getdown_app_dir+"/"+getdown_build_properties
+
     // go through properties looking for getdown_txt_...
     def props = project.properties.sort { it.key }
-    if (JAVA_VERSION.equals("11")) {
-      props.put("getdown_txt_java_min_version", getdown_alt_java11_min_version)
-    } else {
-      props.put("getdown_txt_java_min_version", getdown_alt_java8_min_version)
-    }
+	if (getdown_alt_java_min_version.length() > 0) {
+		props.put("getdown_txt_java_min_version", getdown_alt_java_min_version)
+	}
+	if (getdown_alt_java_max_version.length() > 0) {
+		props.put("getdown_txt_java_max_version", getdown_alt_java_max_version)
+	}
+	props.put("getdown_txt_multi_java_location", getdown_alt_multi_java_location)
+
+    props.put("getdown_txt_appbase", getdown_app_base)
     props.each{ prop, val ->
       if (prop.startsWith("getdown_txt_") && val != null) {
-        // file values rationalised
-        if (val.indexOf('/') > -1) {
-          def r = null
-          if (val.indexOf('/') == 0) {
-            // absolute path
-            r = file(val)
-          } else if (val.indexOf('/') > 0) {
-            // relative path (relative to jalviewDir)
-            r = file( jalviewDir + '/' + val )
+        if (prop.startsWith("getdown_txt_multi_")) {
+          def key = prop.substring(18)
+          val.split(",").each{ v ->
+            def line = key + " = " + v + "\n"
+            getdownTextString += line
           }
-          if (r.exists()) {
-            val = getdown_resource_dir + '/' + r.getName()
-            getdownWebsiteResourceFilenames += val
-            getdownResourceFilenames += r.getPath()
+        } else {
+          // file values rationalised
+          if (val.indexOf('/') > -1 || prop.startsWith("getdown_txt_resource")) {
+            def r = null
+            if (val.indexOf('/') == 0) {
+              // absolute path
+              r = file(val)
+            } else if (val.indexOf('/') > 0) {
+              // relative path (relative to jalviewDir)
+              r = file( jalviewDir + '/' + val )
+            }
+            if (r.exists()) {
+              val = getdown_resource_dir + '/' + r.getName()
+              getdownWebsiteResourceFilenames += val
+              getdownResourceFilenames += r.getPath()
+            }
+          }
+          if (! prop.startsWith("getdown_txt_resource")) {
+            def line = prop.substring(12) + " = " + val + "\n"
+            getdownTextString += line
           }
         }
-        def line = prop.substring(12) + " = " + val + "\n"
-        getdownTextString += line
       }
     }
 
@@ -372,7 +911,7 @@ task getdownWebsite() {
     }
 
     def codeFiles = []
-    makeDist.outputs.files.each{ f ->
+    fileTree(file(packageDir)).each{ f ->
       if (f.isDirectory()) {
         def files = fileTree(dir: f, include: ["*"]).getFiles()
         codeFiles += files
@@ -389,27 +928,36 @@ task getdownWebsite() {
       }
     }
 
+    // NOT USING MODULES YET, EVERYTHING SHOULD BE IN dist
+    /*
     if (JAVA_VERSION.equals("11")) {
-      def j11libFiles = fileTree(dir: "$jalviewDir/$j11libDir", include: ["*.jar"]).getFiles()
-      j11libFiles.sort().each{f ->
-        def line = "code = " + getdown_j11lib_dir + '/' + f.getName() + "\n"
-        getdownTextString += line
-        copy {
-          from f.getPath()
-          into project.ext.getdownJ11libDir
-        }
-      }
+    def j11libFiles = fileTree(dir: "$jalviewDir/$j11libDir", include: ["*.jar"]).getFiles()
+    j11libFiles.sort().each{f ->
+    def line = "code = " + getdown_j11lib_dir + '/' + f.getName() + "\n"
+    getdownTextString += line
+    copy {
+    from f.getPath()
+    into project.ext.getdownJ11libDir
+    }
+    }
     }
+     */
 
-    getdownTextString += "code = " + file(getdownLauncher).getName() + "\n"
+    // getdown-launcher.jar should not be in main application class path so the main application can move it when updated.  Listed as a resource so it gets updated.
+    //getdownTextString += "class = " + file(getdownLauncher).getName() + "\n"
+    getdownTextString += "resource = " + getdown_launcher_new + "\n"
     getdownTextString += "class = " + mainClass + "\n"
 
     def getdown_txt = file(project.ext.getdownWebsiteDir + "/getdown.txt")
     getdown_txt.write(getdownTextString)
 
+    def launch_jvl = file(project.ext.getdownWebsiteDir + "/" + getdown_launch_jvl)
+    launch_jvl.write("appbase="+props.get("getdown_txt_appbase"))
+
     copy {
-      from getdown_txt
-      into project.ext.getdownFilesDir
+      from getdownLauncher
+      rename(file(getdownLauncher).getName(), getdown_launcher_new)
+      into project.ext.getdownWebsiteDir
     }
 
     copy {
@@ -417,36 +965,72 @@ task getdownWebsite() {
       into project.ext.getdownWebsiteDir
     }
 
+    if (! (CHANNEL.startsWith("ARCHIVE") || CHANNEL.startsWith("DEVELOP"))) {
+      copy {
+        from getdown_txt
+        from getdownLauncher
+        from getdownWebsiteDir+"/"+getdown_build_properties
+        into getdownInstallDir
+      }
+
+      copy {
+        from getdownInstallDir
+        into getdownFilesInstallDir
+      }
+    }
+
     copy {
+      from getdown_txt
+      from launch_jvl
       from getdownLauncher
-      into project.ext.getdownFilesDir
+      from getdownWebsiteDir+"/"+getdown_build_properties
+      into getdownFilesDir
     }
 
     copy {
-      from jalviewDir + '/' + project.getProperty('getdown_txt_ui.background_image')
-      from jalviewDir + '/' + project.getProperty('getdown_txt_ui.error_background')
-      from jalviewDir + '/' + project.getProperty('getdown_txt_ui.progress_image')
-      from jalviewDir + '/' + project.getProperty('getdown_txt_ui.icon')
-      from jalviewDir + '/' + project.getProperty('getdown_txt_ui.mac_dock_icon')
-      into project.ext.getdownFilesDir + '/' + getdown_resource_dir 
+	  from getdownResourceDir
+      into project.ext.getdownFilesDir + '/' + getdown_resource_dir
     }
   }
 
-  inputs.dir(jalviewDir + '/' + packageDir)
+  if (buildDist) {
+    inputs.dir(jalviewDir + '/' + packageDir)
+  }
   outputs.dir(project.ext.getdownWebsiteDir)
   outputs.dir(project.ext.getdownFilesDir)
 }
 
 task getdownDigest(type: JavaExec) {
+  group = "distribution"
+  description = "Digest the getdown website folder"
   dependsOn getdownWebsite
-  classpath = files(jalviewDir + '/' + getdown_core)
+  classpath = files(jalviewDir + '/' + getdown_core, jalviewDir+'/'+getdown_launcher)
   main = "com.threerings.getdown.tools.Digester"
   args project.ext.getdownWebsiteDir
+  inputs.dir(project.ext.getdownWebsiteDir)
   outputs.file(project.ext.getdownWebsiteDir + '/' + "digest2.txt")
 }
 
 task getdown() {
+  group = "distribution"
+  description = "Create the minimal and full getdown app folder for installers and website and create digest file"
   dependsOn getdownDigest
+  doLast {
+    if (reportRsyncCommand) {
+      def fromDir = getdownWebsiteDir + (getdownWebsiteDir.endsWith("/")?"":"/")
+      def toDir = getdown_rsync_dest + "/" + getdownDir + (getdownDir.endsWith("/")?"":"/")
+      println "LIKELY RSYNC COMMAND:"
+      println "mkdir -p '$toDir'\nrsync -avh --delete '$fromDir' '$toDir'"
+      if (RUNRSYNC == "true") {
+        exec {
+          commandLine "mkdir", "-p", toDir
+        }
+        exec {
+          commandLine "rsync", "-avh", "--delete", fromDir, toDir
+        }
+      }
+    }
+  }
 }
 
 clean {
@@ -468,14 +1052,172 @@ install4j {
     install4jHomeDir = System.getProperty("user.home")+"/buildtools/install4j"
   }
   installDir = file(install4jHomeDir)
+  mediaTypes = Arrays.asList(install4jMediaTypes.split(","))
+  if (install4jFaster.equals("true")) {
+    faster = true
+  }
+}
+
+def install4jConf
+def macosJavaVMDir
+def macosJavaVMTgz
+def windowsJavaVMDir
+def windowsJavaVMTgz
+def install4jDir = "$jalviewDir/$install4jResourceDir"
+def install4jConfFile = "jalview-installers-java"+JAVA_VERSION+".install4j"
+install4jConf = "$install4jDir/$install4jConfFile"
+
+task copyInstall4jTemplate(type: Copy) {
+  macosJavaVMDir = System.env.HOME+"/buildtools/jre/openjdk-java_vm/getdown/macos-jre"+JAVA_VERSION+"/jre"
+  macosJavaVMTgz = System.env.HOME+"/buildtools/jre/openjdk-java_vm/install4j/tgz/macos-jre"+JAVA_VERSION+".tar.gz"
+  windowsJavaVMDir = System.env.HOME+"/buildtools/jre/openjdk-java_vm/getdown/windows-jre"+JAVA_VERSION+"/jre"
+  windowsJavaVMTgz = System.env.HOME+"/buildtools/jre/openjdk-java_vm/install4j/tgz/windows-jre"+JAVA_VERSION+".tar.gz"
+  from (install4jDir) {
+    include install4jTemplate
+    rename (install4jTemplate, install4jConfFile)
+    filter(ReplaceTokens, beginToken: '', endToken: '', tokens: ['9999999999': JAVA_VERSION])
+    filter(ReplaceTokens, beginToken: '$$', endToken: '$$',
+    tokens: [
+    'JAVA_VERSION': JAVA_VERSION,
+    'JAVA_INTEGER_VERSION': JAVA_INTEGER_VERSION,
+    'VERSION': JALVIEW_VERSION,
+    'MACOS_JAVA_VM_DIR': macosJavaVMDir,
+    'MACOS_JAVA_VM_TGZ': macosJavaVMTgz,
+    'WINDOWS_JAVA_VM_DIR': windowsJavaVMDir,
+    'WINDOWS_JAVA_VM_TGZ': windowsJavaVMTgz,
+    'INSTALL4JINFOPLISTFILEASSOCIATIONS': install4jInfoPlistFileAssociations,
+    'COPYRIGHT_MESSAGE': install4jCopyrightMessage,
+    'MACOS_BUNDLE_ID': install4jMacOSBundleId,
+    'GETDOWN_RESOURCE_DIR': getdown_resource_dir,
+    'GETDOWN_DIST_DIR': getdown_app_dir,
+    'GETDOWN_ALT_DIR': getdown_app_dir_alt,
+    'GETDOWN_INSTALL_DIR': getdown_install_dir
+    ]
+    )
+    if (OSX_KEYPASS=="") {
+      filter(ReplaceTokens, beginToken: 'codeSigning macEnabled="', endToken: '"', tokens: ['true':'codeSigning macEnabled="false"'])
+      filter(ReplaceTokens, beginToken: 'runPostProcessor="true" ',endToken: 'Processor', tokens: ['post':'runPostProcessor="false" postProcessor'])
+    }
+  }
+  into install4jDir
+  outputs.files(install4jConf)
+
+  doLast {
+    // include file associations in installer
+    def installerFileAssociationsXml = file("$install4jDir/$install4jInstallerFileAssociations").text
+    ant.replaceregexp(
+      byline: false,
+      flags: "s",
+      match: '<action name="EXTENSIONS_REPLACED_BY_GRADLE".*?</action>',
+      replace: installerFileAssociationsXml,
+      file: install4jConf
+    )
+    /*
+    // include uninstaller applescript app files in dmg
+    def installerDMGUninstallerXml = file("$install4jDir/$install4jDMGUninstallerAppFiles").text
+    ant.replaceregexp(
+    byline: false,
+    flags: "s",
+    match: '<file name="UNINSTALL_OLD_JALVIEW_APP_REPLACED_IN_GRADLE" file=.*?>',
+    replace: installerDMGUninstallerXml,
+    file: install4jConf
+    )
+     */
+  }
 }
 
 task installers(type: com.install4j.gradle.Install4jTask) {
+  group = "distribution"
+  description = "Create the install4j installers"
   dependsOn getdown
-  projectFile = "$jalviewDir/$install4jResourceDir/$install4jConf"
-  variables = [majorVersion: version.substring(2, 11), build: 001]
-  destination = "$jalviewDir/$install4jBuildDir"
+  dependsOn copyInstall4jTemplate
+  projectFile = file(install4jConf)
+  println("Using projectFile "+projectFile)
+  variables = [majorVersion: version.substring(2, 11), build: 001, OSX_KEYSTORE: OSX_KEYSTORE, JSIGN_SH: JSIGN_SH]
+  destination = "$jalviewDir/$install4jBuildDir/$JAVA_VERSION"
   buildSelected = true
+
+  if (OSX_KEYPASS) {
+    macKeystorePassword=OSX_KEYPASS
+
+  }
+
   inputs.dir(project.ext.getdownWebsiteDir)
-  outputs.dir("$jalviewDir/$install4jBuildDir")
+  inputs.file(install4jConf)
+  inputs.dir(macosJavaVMDir)
+  inputs.dir(windowsJavaVMDir)
+  outputs.dir("$jalviewDir/$install4jBuildDir/$JAVA_VERSION")
+
+}
+
+clean {
+  delete install4jConf
+}
+
+task sourceDist (type: Tar) {
+  
+  def VERSION_UNDERSCORES = JALVIEW_VERSION.replaceAll("\\.", "_")
+  archiveFileName = project.name + "_" + VERSION_UNDERSCORES + ".tar.gz"
+  
+  compression Compression.GZIP
+  
+  from jalviewDir
+  into project.name
+ 
+   
+  exclude (".*")
+  exclude ("**/.*")
+  exclude ("*.class")
+  exclude ("**/*.class")
+  include (eclipse_extra_jdt_prefs_file)
+  include ("AUTHORS")
+  include ("CITATION")
+  include ("FEATURETODO")
+  include ("JAVA-11-README")
+  include ("FEATURETODO")
+  include ("LICENSE")
+  include ("README")
+  include ("RELEASE")
+  include ("THIRDPARTYLIBS")
+  include ("build.gradle")
+  include ("gradle.properties")
+  include ("$sourceDir/*.java")
+  include ("$sourceDir/**/*.java")
+  include ("$sourceDir/**/*.cdr")
+  include ("$j8libDir/**/*.jar")
+  include ("$j11libDir/**/*.jar")
+  include ("$resourceDir/**/*")
+  include ("$helpDir/**/*")
+  include ("$schemaDir/**/*")
+  include ("$utilsDir/**/*")
+  include ("$docDir/**/*")
+  include ("$examplesDir/**/*")
+  include ("getdown/**/*")
+  //include ("jalview-jalopy.xml")
+  //include ("JalviewApplet.jpx")
+  //include ("JalviewX.jpx")
+  //include ("nbbuild.xml")
+  //include ("nbproject/genfiles.properties")
+  //include ("nbproject/project.properties")
+  //include ("nbproject/project.xml")
+  
+  exclude ("appletlib")
+  exclude ("**/*locales")
+  exclude ("*locales/**")
+  exclude ("utils/InstallAnywhere")
+  exclude (libDir)
+  exclude (getdown_files_dir)
+  exclude (getdown_website_dir)
+
+  // exluding these as not using jars as modules yet
+  exclude ("$j11modDir/**/*.jar")
+
+}
+
+task helppages  {
+  dependsOn copyHelp
+  dependsOn pubhtmlhelp
+  
+  inputs.dir("$classes/$helpDir")
+  outputs.file("build/distribution/help/helpTOC.html")
 }