still some sort of issue running git here

build.gradle

@@ -1,8 +1,6 @@
 //import org.ajoberstar.grgit.*
 //import org.ajoberstar.gradle.git.tasks.*
 
-
-
 /*
  * This build file was auto generated by running the Gradle 'init' task
  * by 'nathandunn' at '3/14/16 12:08 PM' with Gradle 2.11
@@ -13,15 +11,16 @@
  */
 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 {
@@ -55,7 +54,7 @@ task evaluateJBrowseConfigs {
     jbrowsePlugins = jbrowseConfig.plugins
     // if apollo-config.groovy exists, read THAT in and apply it as well
     File testFile = new File("apollo-config.groovy")
-    if(testFile){
+    if (testFile) {
         def revisedConfig = new ConfigSlurper().parse(new File("apollo-config.groovy").toURI().toURL())
         jbrowseConfig = revisedConfig.jbrowse ?: jbrowseConfig
         jbrowsePlugins << revisedConfig.jbrowse.plugins
@@ -65,7 +64,7 @@ task evaluateJBrowseConfigs {
     println "final plugins ${jbrowsePlugins}"
 }
 
-task copyResourcesDev(dependsOn:"copy-resources-dev") << {
+task copyResourcesDev(dependsOn: "copy-resources-dev") << {
 
 }
 
@@ -81,7 +80,7 @@ task installJBrowse(dependsOn: "setup-jbrowse") << {
 //    copyResourcesDev.execute()
 }
 
-task setupJBrowse(dependsOn:"setup-jbrowse") << { }
+task setupJBrowse(dependsOn: "setup-jbrowse") << {}
 
 //task cloneGitRepo(type: GitClone) {
 //    def destination = file("abcd")
@@ -91,78 +90,72 @@ task setupJBrowse(dependsOn:"setup-jbrowse") << { }
 //    enabled = !destination.exists() //to clone only once
 //}
 
-task cloneGitExec(type: Exec) << {
-    println "TRYING TO CLOEN ${currentPlugin}"
-    if(currentPlugin){
+task cloneGitExec(type: Exec) {
+    onlyIf { Task task ->
+        println "TRYING TO CLOEN ${currentPlugin}"
         workingDir "jbrowse-download/plugins/${currentPlugin.key}"
 
         println "CLONNING "
-        execCommand "git"
-        commandLine "clone",currentPlugin.value.git
+//        execCommand "git"
+        commandLine "git", "clone", currentPlugin.value.git
         println "CLONED ABC"
         standardOutput = new ByteArrayOutputStream()
         println "STARNDARD OUTPUT ${standardOutput}"
-    }
-    else{
-        execCommand ""
+        return currentPlugin != null
     }
 }
 
-task installJBrowsePlugins <<  {
+
+task installJBrowsePlugins << {
     println "installing jbrowse plugins  ${jbrowsePlugins}"
 
-    for(plugin in jbrowsePlugins){
+    for (plugin in jbrowsePlugins) {
         currentPlugin = plugin
         println "KEY ${plugin.key}"
         println "GIT ${plugin.value}"
-        def path = pluginsDirectory+"/"+plugin.key
+        def path = pluginsDirectory + "/" + plugin.key
         def pluginExists = confirmPlugin(path)
-        if(plugin.value.included==true){
-            if(pluginExists){
+        if (plugin.value.included == true) {
+            if (pluginExists) {
                 println "Plugin ${path} exists and appears valid."
-            }
-            else{
+            } else {
                 println "ERROR: There is a problem with the plugin at ${path}!"
             }
-        }
-        else
-        if(plugin.value.git){
+        } else if (plugin.value.git) {
             println "is GIT"
-            if(pluginExists){
+            if (pluginExists) {
                 println "Plugin ${path} exists and appears valid."
                 println "git pull if alwaysPull"
                 println "git checkout proper directory"
-            }
-            else{
+            } 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){
+                if (currentPlugin) {
                     cloneGitExec.execute()
+                    File testFile = new File(".")
+                    "/usr/bin/git clone ${plugin.value.git}".execute(null,testFile)
                 }
                 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){
+        } else if (plugin.value.url == true) {
+            if (!pluginExists) {
                 println "Plugin ${path} exists and appears valid."
             }
-        }
-        else{
+        } else {
             println "not included . . requiring action"
         }
     }
 }
 
 // root task
-task handleJBrowse (dependsOn:['evaluateJBrowseConfigs','installJBrowse','installJBrowsePlugins',"copyResourcesDev"]) <<{
+task handleJBrowse(dependsOn: ['evaluateJBrowseConfigs', 'installJBrowse', 'installJBrowsePlugins', "copyResourcesDev"]) << {
     println "handling jbrowse ${jbrowseConfig}"
 
 }