got a working clone

build.gradle

@@ -1,5 +1,4 @@
-//import org.ajoberstar.grgit.*
-//import org.ajoberstar.gradle.git.tasks.*
+import org.ajoberstar.grgit.*
 
 /*
  * This build file was auto generated by running the Gradle 'init' task
@@ -9,18 +8,15 @@
  * For more details take a look at the Java Quickstart chapter in the Gradle
  * user guide available at https://docs.gradle.org/2.11/userguide/tutorial_java_projects.html
  */
-ant.importBuild 'build.xml'
-
-// Apply the java plugin to add support for Java
-apply plugin: 'java'
-apply plugin: 'groovy'
-apply plugin: 'eclipse'
-apply plugin: 'idea'
 
-//buildscript {
-//    repositories { mavenCentral() }
-//    dependencies { classpath 'org.ajoberstar:gradle-git:1.4.2' }
-//}
+buildscript {
+    repositories {
+        mavenCentral()
+    }
+    dependencies {
+        classpath 'org.ajoberstar:gradle-git:1.4.2'
+    }
+}
 
 // In this section you declare where to find the dependencies of your project
 repositories {
@@ -29,6 +25,16 @@ repositories {
     jcenter()
 }
 
+
+ant.importBuild 'build.xml'
+
+// Apply the java plugin to add support for Java
+apply plugin: 'java'
+apply plugin: 'groovy'
+apply plugin: 'eclipse'
+apply plugin: 'idea'
+//apply plugin: "de.qaware.seu.as.code.git"
+
 // In this section you declare the dependencies for your production and test code
 dependencies {
     // The production code uses the SLF4J logging API at compile time
@@ -47,6 +53,18 @@ def jbrowsePlugins
 def pluginsDirectory = "jbrowse-download/plugins"
 def currentPlugin
 
+
+task cloneTask(type: CloneTask)
+
+class CloneTask extends DefaultTask {
+
+    @TaskAction
+    def clone() {
+        def grgit = Grgit.clone(dir: 'asdf', uri: 'https://github.com/GMOD/myvariantviewer')
+    }
+}
+
+
 task evaluateJBrowseConfigs {
     // gradle read in Config.groovy
     def config = new ConfigSlurper().parse(new File("grails-app/conf/Config.groovy").toURI().toURL())
@@ -82,37 +100,12 @@ task installJBrowse(dependsOn: "setup-jbrowse") << {
 
 task setupJBrowse(dependsOn: "setup-jbrowse") << {}
 
-//task cloneGitRepo(type: GitClone) {
-//    def destination = file("abcd")
-//    uri = "https://github.org/GMOD/myvariantviewer"
-//    destinationPath = destination
-//    bare = false
-//    enabled = !destination.exists() //to clone only once
-//}
-
-task cloneGitExec(type: Exec) {
-    onlyIf { Task task ->
-        println "TRYING TO CLOEN ${currentPlugin}"
-        workingDir "jbrowse-download/plugins/${currentPlugin.key}"
-
-        println "CLONNING "
-//        execCommand "git"
-        commandLine "git", "clone", currentPlugin.value.git
-        println "CLONED ABC"
-        standardOutput = new ByteArrayOutputStream()
-        println "STARNDARD OUTPUT ${standardOutput}"
-        return currentPlugin != null
-    }
-}
-
 
 task installJBrowsePlugins << {
     println "installing jbrowse plugins  ${jbrowsePlugins}"
 
     for (plugin in jbrowsePlugins) {
         currentPlugin = plugin
-        println "KEY ${plugin.key}"
-        println "GIT ${plugin.value}"
         def path = pluginsDirectory + "/" + plugin.key
         def pluginExists = confirmPlugin(path)
         if (plugin.value.included == true) {
@@ -129,20 +122,12 @@ task installJBrowsePlugins << {
                 println "git checkout proper directory"
             } else {
                 println "git clone to the proper directory"
-//                def grgit = Grgit.clone(dir: pluginsDirectory, uri: '[email protected]:ajoberstar/grgit.git')
                 println "cloning from ${plugin.value.git} into ${path}"
                 currentPlugin = plugin
-//                tasks["cloneGitExec"].execute()
-                if (currentPlugin) {
-                    cloneGitExec.execute()
-                    File testFile = new File(".")
-                    "/usr/bin/git clone ${plugin.value.git}".execute(null,testFile)
-                }
+                println "current plugin ${currentPlugin}"
+                println "attemptping to clone from '${plugin.value.git}' into '${path}'"
+                def grgit = Grgit.clone(dir: path , uri: plugin.value.git)
                 println "CLONED from ${plugin.value.git} into ${path}"
-
-//                def grgit = Grgit.clone(dir: path, uri: plugin.value.git)
-//                def grgit = Grgit.clone(dir: "ASdf", uri: plugin.value.git)
-//                ["git","clone",plugin.value.git].execute()
             }
         } else if (plugin.value.url == true) {
             if (!pluginExists) {
@@ -163,4 +148,5 @@ task handleJBrowse(dependsOn: ['evaluateJBrowseConfigs', 'installJBrowse', 'inst
 def confirmPlugin(String path) {
     File file = new File(path)
     return file.exists() && file.isDirectory() && file.canRead()
-}
+}
+

gradle/wrapper/gradle-wrapper.properties

@@ -1,6 +1,6 @@
-#Mon Mar 14 12:08:11 PDT 2016
+#Mon Mar 14 22:13:59 PDT 2016
 distributionBase=GRADLE_USER_HOME
 distributionPath=wrapper/dists
 zipStoreBase=GRADLE_USER_HOME
 zipStorePath=wrapper/dists
-distributionUrl=https\://services.gradle.org/distributions/gradle-2.11-bin.zip
+distributionUrl=https\://services.gradle.org/distributions/gradle-2.11-all.zip

grails-app/conf/Config.groovy

@@ -368,7 +368,7 @@ jbrowse {
             included = true
         }
         MyVariantInfo {
-            git = 'https://github.org/GMOD/myvariantviewer'
+            git = 'https://github.com/GMOD/myvariantviewer'
 //            git = '[email protected]:GMOD/myvariantviewer.git'
             branch = 'master'
             alwaysRecheck = "true"