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