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
.