Biopet Project
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
-
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
-
In the root directory:
mvn install
-
Go to the Biopet root directory and run:
mvn install
If you want to use the prebuilt Queue JAR downloaded from the website
-
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
-
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.