Bioinformatics and Docker

Bioinformatics and Docker

Since it is our lightweight algorithm day, we thought it would be worthwhile to mention several relevant posts on Docker.

1. What is Docker?

Docker is a lightweight way to introduce portability in the code. It helps you containerize a code module tested on an operating system, and not run a separate VMware virtualization installation for every new module.

The following slides introduce you to Docker. Especially pay attention to the ‘matrix from hell’ slide.

[slideshare id=27669368&doc;=introdockeroctober13-131028203253-phpapp02]

2. Docker in Bioinformatics

Docker is being used to containerize bioinformatics codes and there is already a biodocker project.

A few days back, redditers asked - Does Docker hit performance of bioinformatics algorithms?

The following blog post from Heng Li would be informative in that respect.

A few hours with docker

Preliminary thoughts

Docker is a bless to complex systems such as the old Apache+MySQL+PHP combo, but is a curse to simple command line tools. For simple tools, it adds multiple complications (security, kernel version, Dockerfile, large package, inter-process communication, etc) with little benefit.

Bioinformatics tools are not rocket science. They are supposed to be simple. If they are not simple, we should encourage better practices rather than live with the problems and resort to docker. I am particularly against dockerizing easy-to-compile tools such as velvet and bwa or well packaged tools such as spades. Another large fraction of tools in C/C++ can be compiled to statically linked binaries or shipped with necessary dynamic libraries (see salifish). While not ideal, these are still better solutions than docker. Docker will be needed for some tools with complex dependencies, but I predict most of such tools will be abandoned by users unless they are substantially better than other competitors, which rarely happens in practice.

PS: the only benefit of dockerizing simple tools is that we can acquire a tool with docker pull user/tool, but that is really the benefit of a centralized repository which we are lacking in our field.

Our view is in agreement with Heng Li’s last paragraph (“PS”), but Docker will likely have a different use in the bioinformatics world. More on that in a later blog post.



Adding a few other useful links -

1. Dockerized bioinformatics programs at biostar

2. Benchmarking variation and RNA-seq analyses on Amazon Web Services with Docker

We developed a freely available, easy to run implementation of bcbio-nextgen on Amazon Web Services (AWS) using Docker. bcbio is a community developed tool providing validated and scalable variant calling and RNA-seq analysis. The AWS implementation automates all of the steps of building a cluster, attaching high performance shared filesystems, and running an analysis. This makes bcbio readily available to the research community without the need to install and configure a local installation.

The entire installation bootstraps from standard Linux AMIs, enabling adjustment of the tools, genome data and installation without needing to prepare custom AMIs. The implementation uses Elasticluster to provision and configure the cluster. We automate the process with the boto Python interface to AWS and Ansible scripts. bcbio-vm isolates code and tools inside a Docker container allowing runs on any remote machine with a download of the Docker image and access to the shared filesystem. Analyses run directly from S3 buckets, with automatic streaming download of input data and upload of final processed data.

We provide timing benchmarks for running a full variant calling analysis using bcbio on AWS. The benchmark dataset was a cancer tumor/normal evaluation, from the ICGC-TCGA DREAM challenge, with 100x coverage in exome regions. We compared the results of running this dataset on 2 different networked filesystems: Lustre and NFS. We also show benchmarks for an RNA-seq dataset using inputs from the Sequencing Quality Control (SEQC) project.

3. Docker guide at basespace

Written by M. //