H3ABioNet Hackathon (Workflows)

Wed, 24 Aug 2016 07:40:04 -0700
biology, debian, tech, workflows

I'm in Pretoria, South Africa at the H3ABioNet hackathon which is developing workflows for Illumina chip genotyping, imputation, 16S rRNA sequencing, and population structure/association testing. Currently, I'm working with the imputation stream and we're using Nextflow to deploy an IMPUTE-based imputation workflow with Docker and NCSA's openstack-based cloud (Nebula) underneath.

The OpenStack command line clients (nova and cinder) seem to be pretty usable to automate bringing up a fleet of VMs and the cloud-init package which is present in the images makes configuring the images pretty simple.

Now if I just knew of a better shared object store which was supported by Nextflow in OpenStack besides mounting an NFS share, things would be better.

You can follow our progress in our git repo: [https://github.com/h3abionet/chipimputation]