From 90000b66cd302f993418abf217acaa798573c505 Mon Sep 17 00:00:00 2001 From: Don Armstrong Date: Wed, 24 Aug 2016 07:39:45 -0700 Subject: [PATCH] add post on H3ABioNet Hackathon --- posts/h3a_bionet_worfklowhackathon.mdwn | 29 +++++++++++++++++++++++++ 1 file changed, 29 insertions(+) create mode 100644 posts/h3a_bionet_worfklowhackathon.mdwn diff --git a/posts/h3a_bionet_worfklowhackathon.mdwn b/posts/h3a_bionet_worfklowhackathon.mdwn new file mode 100644 index 0000000..69712dd --- /dev/null +++ b/posts/h3a_bionet_worfklowhackathon.mdwn @@ -0,0 +1,29 @@ +[[!meta title="H3ABioNet Hackathon (Workflows)"]] + +I'm in Pretoria, South Africa at the +[H3ABioNet](http://h3abionet.org/) +[hackathon](http://h3abionet.org/17-h3abionet-courses/h3abionet-courses-upcoming/266-h3abionet-cloud-computing-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](https://www.nextflow.io/) to deploy an +[IMPUTE](https://mathgen.stats.ox.ac.uk/impute/impute_v2.html)-based +imputation workflow with Docker and +[NCSA's openstack-based cloud (Nebula)](https://wiki.ncsa.illinois.edu/display/NEBULA/Nebula+Home) +underneath. + +The OpenStack command line clients (`nova` and `cinder`) seem to be +pretty usable to +[automate bringing up a fleet of VMs](https://github.com/h3abionet/chipimputation/blob/master/openstack/generate_openstack) +and the cloud-init package which is present in the images makes +[configuring the images pretty simple](https://github.com/h3abionet/chipimputation/tree/master/openstack). + +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 + + +[[!tag debian tech biology workflows]] -- 2.39.2