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Last pushed: 2 years ago
Short Description
A genomics processing engine and file format built using Apache Spark. http://bdgenomics.org/
Full Description

ADAM: Avro Data Alignment Map

Supported tags and respective Dockerfile links

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

2) 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
Docker Pull Command
Owner
gelog
Source Repository

Comments (1)
flankw
a year ago

docker run --rm=true -ti -v $HOME/data/:/data