add post on H3ABioNet Hackathon
authorDon Armstrong <don@donarmstrong.com>
Wed, 24 Aug 2016 14:39:45 +0000 (07:39 -0700)
committerDon Armstrong <don@donarmstrong.com>
Wed, 24 Aug 2016 14:39:45 +0000 (07:39 -0700)
posts/h3a_bionet_worfklowhackathon.mdwn [new file with mode: 0644]

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+[[!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]]