Fix dir

README.md

@@ -65,7 +65,7 @@ To develop Biopet, Java 7, Maven 3.2.2, and GATK Queue 3.4 is required. Please c
 
 ~~~
 $ git clone https://github.com/broadgsa/gatk-protected
-$ cd gatk
+$ cd gatk-protected
 $ git checkout 3.4                              # the current release is based on GATK 3.4
 $ mvn -U clean install
 ~~~

docs/index.md

@@ -65,9 +65,9 @@ To develop Biopet, Java 7, Maven 3.2.2, and GATK Queue 3.4 is required. Please c
 
 ~~~
 $ git clone https://github.com/broadgsa/gatk-protected
-$ cd gatk
+$ cd gatk-protected
 $ git checkout 3.4                              # the current release is based on GATK 3.4
-$ mvn -U clean install
+$ mvn clean install
 ~~~
 
 This will install all the required dependencies to your local maven repository. After this is done, you can clone our repository and test if everything builds fine:
@@ -75,7 +75,7 @@ This will install all the required dependencies to your local maven repository.
 ~~~
 $ git clone https://github.com/biopet/biopet.git
 $ cd biopet
-$ mvn -U clean install
+$ mvn clean install
 ~~~
 
 If everything builds fine, you're good to go! Otherwise, don't hesitate to contact us or file an issue at our issue tracker.