Merge branch 'patch_readme' into 'master'

README updates

README updates with installation notes (includes non-SHARK and SHARK installs)

README.md

-Biopet project
-=======================
+Biopet Project
+==============
 
-Framework build on top of GATK Queue for building bioinformatic pipelines
+Framework build on top of GATK Queue for building bioinformatic pipelines.
+
+
+Installation
+============
+
+Note: all installation procedures require Maven.
+
+### If you are in SHARK or have access to SHARK directories
+
+Run the `mvn_install_queue.sh` script
+
+### Non-SHARK installs
+
+#### If you want to build Queue via the repository
+
+1. Clone the GATK protected repository. We need to use the protected repository because some pipelines use the GATK walkers.
+
+    git clone git@github.com:broadgsa/gatk-protected.git
+
+2. In the root directory:
+
+    mvn install
+
+3. Go to the Biopet root directory and run:
+
+    mvn install
+
+#### If you want to use the prebuilt Queue JAR downloaded from the website
+
+1. Install the Queue JAR in your local maven repository:
+
+    mvn install:install-file -Dfile={your_queue_jar} -DgroupId=org.broadinstitute.sting -DartifactId=queue-package -Dversion={your_queue_version} -Dpackaging=jar
+
+2. Go to the Biopet root directory and run:
+
+    mvn install
 
 
 License
-===
+=======
 
-A dual licensing mode is applied. The source code within this project is freely available for non-commercial use under an AGPL license; For commercial users or users who do not want to follow the AGPL license, please contact sasc@lumc.nl to purchase a separate license.
\ No newline at end of file
+A dual licensing mode is applied. The source code within this project is freely available for non-commercial use under an AGPL license; For commercial users or users who do not want to follow the AGPL license, please contact [sasc@lumc.nl](mailto:sasc@lumc.nl) to purchase a separate license.