docker-ubuntu-avocado's Introduction

Supported tags and respective `Dockerfile` links

What is Avocado ?

avocado is a distributed pipeline for calling variants, and is built on top of Apache Spark and the ADAM API. avocado provides a highly configurable pipeline that can be used for the alignment, processing, and variant calling of genomes/exomes/targets. We are currently in the process of hardening avocado for clincial use, and expanding the avocado pipeline so that it can triage processing steps based on genomic complexity.

avocado is on Github, and is in active development.

http://bdgenomics.org/projects/avocado/

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/

Dependencies

Install Docker

Base Docker image

gelog/spark:1.1.0-bin-hadoop2.3

How to use this image?

1) Get the adam file of a genome (or chromosome)

1.1) Get it from Adam

2) Get the reference genome (or chromosome) and unzip it.

mkdir /data/
wget -O /data/chr1.fa.gz http://hgdownload.cse.ucsc.edu/goldenPath/hg19/chromosomes/chr1.fa.gz
gzip -d /data/chr1.fa.gz

3) Find the variation of the genome (or chromosome) with Avocado

docker run -ti --rm --name client-genomics -v /data:/data gelog/avocado /bin/bash
avocado-submit /data/SRR062634.adam /data/chr1.fa /data/SRR062634.avr /usr/local/avocado/avocado-sample-configs/basic.properties

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docker-ubuntu-avocado's Issues

OutOfMemoryError

Error:

2015-03-22 17:29:25 ERROR Executor:96 - Exception in task 0.0 in stage 1.0 (TID 16)
java.lang.OutOfMemoryError: GC overhead limit exceeded

Step to reproduce:

docker run -ti --rm --name client-genomics -v /data:/data gelog/avocado /bin/bash avocado-submit /data/SRR062634.adam /data/chr1.fa /data/SRR062634.avr /usr/local/avocado/avocado-sample-configs/basic.properties

You can get the files by following the step from :

snap
adam

avocado-submit crash on startup with insufficient memory

We need to validate that the image is OK to rule out that the problem is only related to missing memory on my old laptop.

Steps to reproduce:

Build the image: docker build --rm=true -t avocado .
Run the container: docker run --rm=true avocado

Error:

Java HotSpot(TM) 64-Bit Server VM warning: INFO: os::commit_memory(0x00000006fff80000, 2863661056, 0) failed; error='Cannot allocate memory' (errno=12)
#
# There is insufficient memory for the Java Runtime Environment to continue.
# Native memory allocation (malloc) failed to allocate 2863661056 bytes for committing reserved memory.
# An error report file with more information is saved as:
# //hs_err_pid40.log

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