Running Mango from Distribution

Fetching Mango Distribution

Mango is packaged as an überjar and includes all necessary dependencies, except for Apache Hadoop and Apache Spark.

To fetch the Mango distribution, run:

VERSION=0.0.3

wget -O mango-distribution-${VERSION}-bin.tar.gz https://search.maven.org/remotecontent?filepath=org/bdgenomics/mango/mango-distribution/${VERSION}/mango-distribution-${VERSION}-bin.tar.gz
tar xzvf mango-distribution-${VERSION}-bin.tar.gz

From the distribution directory, you can run Mango notebook or Mango browser:

First, make sure your SPARK_HOME env variable is set:

export SPARK_HOME=<PATH_TO_SPARK>

Then run Mango notebook or Mango browser:

cd mango-distribution-${VERSION}
./bin/mango-notebook
./bin/mango-submit

Installing python modules

To run Mango in a python notebook, install bdgenomics.mango.pileup, a Jupyter Widget:

pip install bdgenomics.mango.pileup
jupyter nbextension enable --py --sys-prefix bdgenomics.mango.pileup  # can be skipped for notebook version 5.3 and above

And bdgenomics.mango:

pip install bdgenomics.mango