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Last pushed: a year ago
Short Description
ADAM Docker Image
Full Description

ADAM Docker Image

ADAM is a genomics analysis platform with specialized file formats built using Apache Avro, Apache Spark and Parquet. Apache 2 licensed.

This image builds ADAM from the latest source by following official installation instruction. It is build with Apache Spark 1.6.2.

Sample Usage

docker run --rm -t ljishen/adam

This command displays all available commands under adam-submit by default.

Running ADAM

Now you can try running some simple ADAM commands:

transform

Make a sample .adam file like this

docker run --rm -t -v `pwd`:/tmp ljishen/adam adam-submit transform /root/adam/adam-core/src/test/resources/small.sam /tmp/small.adam
flagstat

If you generated the .adam file followed along above, you can gather statistics from this ADAM file

docker run --rm -t -v `pwd`:/tmp ljishen/adam adam-submit flagstat /tmp/small.adam
adam-shell

You can also use adam-shell, here is an example

docker run --rm -t ljishen/adam adam-shell -i kmer.scala

Counting K-mers

You can run the Counting K-mers example from official instruction like this

$ docker run --rm -t -v `pwd`:/tmp ljishen/adam adam-submit count_kmers /tmp/small.adam /tmp/kmers.adam 10
$ head `pwd`/kmers.adam/part-*
(AATTGGCACT,1)
(TTTTAAGGTT,1)
(GAGCAGCCTT,1)
(CCTGCTGTAT,1)
(TTTGTTTGTT,2)
(TTCCGATTTT,1)
(GGCCAGGACT,1)
(GCAGTCCCTC,1)
(AACTTTGAAT,1)
(GATGACGTGG,1)
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ljishen
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