Setup a Bioinformatics Demultiplex Server from Scratch

bioinformatics easybuild hpc Nov 06, 2019

Install Demultiplex Software

Installing demultiplexing such as bcl2fastq, CellRanger, LongRanger, demuxlet, and whatever else pops up, holds a special place in those that do Bioinformatics and Genomics hearts and potential support groups. It has been enough of an issue in my professional life that I thought I would dedicate a series to setting up servers for different analysis types.

Don't install system packages

This is my big chance to go on a total rant about bioinformatics servers!

Don't install all kinds of software as system packages. Ok? Just don't do it. It may not backfire on you today, or tomorrow, but someday it will!

I'm going to make a few caveats to that. Things like zlib, openssl, and ssh are fine. I'll even cheat sometimes and yum install some development tools. Mostly, what I am talking about here is bioinformatics software. Don't bother installing bcl2fastq, blast, augustus, R, python, dask, or pretty much anything else as system dependencies.

There are better...

AWS Elastic Compute Clusters for Genomics

aws bioinformatics hpc Oct 30, 2019

Amazon Web Services (AWS) gives you the ability to build out all kinds of cool infrastructure. Databases, web servers, Kubernetes backed applications, Spark clusters, machine learning models, and even High-Performance Computing Clusters with AWS ParallelCluster.

Not just clusters, but Elastic Clusters!

One of the cooler aspects of using a cloud provider like AWS is the ability to scale up and down based on requests or need. This is generally called Elastic, and applies to a whole lot of services. Storage, Kubernetes, load balancers, and compute clusters. This is first of all just awesome, because writing up something to scale up or down based on demand would be a major pain, and can give the best of all worlds.

Example Genomic Analysis Computional Needs

Let's say you're running a genomics analysis. First, you run your alignment, which takes (for the sake of argument) 20 nodes. Then you do variant calling, which takes 5 compute nodes, haplotype...

Deploy HPC Modules From Bioconda Packages

bioinformatics easybuild hpc Oct 27, 2019

The Struggle is Real

I have been working in Bioinformatics for nearly 10 years, mostly on the computational side of things. I have spent a lot of that time building and installing software. Some of those wounds will never heal! Luckily, along came Anaconda, the scientific distribution of Python, along with the awesome BioConda who took on the task of installing bioinformatics software with relative ease! I don't know if Anaconda necessarily wanted to make life easier for those installing software on HPC systems, but in any case they did.

(Disclaimer, I am technically a core team member of BioConda, but I'm really kind of a slacker core member and the real credit goes to the rest of the team!)

Deploy Modules with EasyBuild

One of my main goals in life is to deploy conda packages as HPC Modules. Deploying HPC Modules can be a bit of a pain. There are a lot of naming conventions, environmental variables, file permissions, recursive file...

Dask on HPC

dask distributed computing hpc parallel computing python Sep 25, 2019

Recently I saw that Dask, a distributed Python library, created some really handy wrappers for running Dask projects on a High-Performance Computing Cluster, HPC.

Most people who use HPC are pretty well versed in technologies like MPI, and just generally abusing multiple compute nodes all at once, but I think technologies like Dask are really going to be game-changers in the way we all work. Because really, who wants to write MPI code or vectorize?

If you've never heard of Dask and it's awesomeness before, I think the easiest way to get started is to look at their Embarrassingly Parallel Example, and don't listen to the haters who think speeding up for loops is lame. It's a superpower!

Onward with examples!

Client and Scheduler

Firstly, these are all pretty much borrowed from the Dask Job Queues page. Pretty much, what you do, is you write your Python code as usual. Then, when you need to scale across nodes you leverage your HPC scheduler to get you some...

Apache Airflow Project Template

Build out your Data Science with Apache Airflow.

Build custom docker images
Bring up your stack with one command
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Deploy to Kubernetes with Helm using a ready made Helm chart.

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Deploy Kubernetes on AWS with:

Terraform - infrastructure as code to give you a repeatable recipe for your Kubernetes deployment
Detailed documentation
Get setup up with a configurable cluster that can be deployed for different projects, or environments (dev/stage/prod)

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This guide provides you with a birds eye view of which AWS services to use for:

Exploratory analyses
Production pipelines
Data visualization platforms (including RShiny and Dash)
and Machine Learning Pipelines

These are the services that I use every day to deploy Bioinformatics related infrastructure.

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