gelog/adam repository overview

⁠ADAM: Avro Data Alignment Map

⁠

⁠Supported tags and respective Dockerfile links

• 0.14.0 (Dockerfile)⁠
• 0.15.0 (Dockerfile)⁠
• 0.16.0 (Dockerfile)⁠
• 0.17.1 (Dockerfile)⁠
• 0.18.0, latest (Dockerfile)⁠

⁠What is Adam ?

ADAM provides both an application programming interface (API) and a command line interface (CLI) for manipulating genomic data on a computing cluster. ADAM operates on data stored inside of Parquet⁠ with the bdg-formats⁠ schemas, using Apache Spark⁠, and provides scalable performance on clusters larger than 100 machines.

ADAM is on Github⁠. Quick start guides are available for running ADAM on EC2⁠, and for building ADAM for specific CDH releases⁠.

http://bdgenomics.org/projects/adam/⁠

⁠What is Docker?

Docker is an open platform for developers and sysadmins to build, ship, and run distributed applications. Consisting of Docker Engine, a portable, lightweight runtime and packaging tool, and Docker Hub, a cloud service for sharing applications and automating workflows, Docker enables apps to be quickly assembled from components and eliminates the friction between development, QA, and production environments. As a result, IT can ship faster and run the same app, unchanged, on laptops, data center VMs, and any cloud.

https://www.docker.com/whatisdocker/⁠

⁠What is a Docker Image?

Docker images are the basis of containers. Images are read-only, while containers are writeable. Only the containers can be executed by the operating system.

https://docs.docker.com/terms/image/⁠

⁠How to use this image?

⁠Converting a BAM / SAM file to the ADAM format

1. (Optional step) Download a small SAM file, if you don't have one handy.

mkdir -p $HOME/data
wget -O $HOME/data/small.sam \
    https://raw.githubusercontent.com/bigdatagenomics/adam/master/adam-core/src/test/resources/small.sam

1. Convert to the ADAM format in a new Adam container

docker run --rm=true -ti -v /data/:/data gelog/adam \
    adam-submit transform \
    $HOME/data/small.sam \
    $HOME/data/small.adam

⁠Known issues

https://github.com/GELOG/docker-ubuntu-adam/issues⁠

⁠Docker Image Hierarchy

• gelog/adam:0.16.0
  • gelog/spark:1.2-bin-hadoop2.3
    • gelog/java:openjdk7