Running Mango from Docker

Running Mango from Docker requires Docker to be installed.

Mango is available on Docker and is available at quay.io.

To pull the Mango docker container, run:

docker pull quay.io/bigdatagenomics/mango:latest

Running Mango Browser on Docker

To run Mango browser example files on Linux in Docker run:

To run Mango browser on local data, you must first mount these files with the Docker -v flag. For example, if you have local files stored at <example-file-path>:

LOCAL_EXAMPLE_FILES=<path_to_example_files>
DOCKER_EXAMPLE_FILES=<path_in_docker_container>

docker run -it -p 8080:8080 \
    -v $LOCAL_EXAMPLE_FILES:$DOCKER_EXAMPLE_FILES \
    --entrypoint=mango-submit \
    quay.io/bigdatagenomics/mango:latest \
    -- $DOCKER_EXAMPLE_FILES/<genome_build_filepath> \
    -reads $DOCKER_EXAMPLE_FILES/<alignment_filepaths> \
    -variants $DOCKER_EXAMPLE_FILES/<variant_filepaths>

To create a genome build (<genome_build_filepath>), see Building a Genome.

Running Mango Notebook on Docker

To run Mango notebook on Linux in Docker run:

docker run --net=host -it -p 8888:8888 \
    --entrypoint=mango-notebook \
    quay.io/bigdatagenomics/mango:latest \
    -- --ip=0.0.0.0 --allow-root

Note: To run the Mango notebook on OS X, remove --net=host.

To view a number of ipython notebook examples, see our github.

Creating a Mango genome using Docker

To run create a mango genome on Linux in Docker run:

LOCAL_LOCATION=<host_src>
DOCKER_LOCATION=<docker_src>
GENOME_BUILD=<genome_name> # i.e. hg19, mm10, etc.

docker run --net=host -it -p 8888:8888 \
    -v $LOCAL_LOCATION:$DOCKER_LOCATION \
    --entrypoint=make_genome \
    quay.io/bigdatagenomics/mango:latest $GENOME_BUILD $DOCKER_LOCATION

The genome file will be saved to <host_src>.

Note: To run the make_genome on OS X, remove --net=host.