From 08f6ea1e6a4edc0bce06b89e19f1a863df5e8a41 Mon Sep 17 00:00:00 2001
From: Don Armstrong <don@donarmstrong.com>
Date: Thu, 22 Sep 2016 14:58:14 -0700
Subject: [PATCH] update h3abionet hackathon

---
 h3abionet_hackathon.Rnw | 63 +++++++++++++++++++++++++++++++++++++++--
 1 file changed, 60 insertions(+), 3 deletions(-)

diff --git a/h3abionet_hackathon.Rnw b/h3abionet_hackathon.Rnw
index ffc730e..c57a6c6 100644
--- a/h3abionet_hackathon.Rnw
+++ b/h3abionet_hackathon.Rnw
@@ -78,28 +78,85 @@
 \section{Location}
 
 \begin{frame}{Pretoria}
+\includegraphics[width=\textwidth,keepaspectratio]{photos/pano.jpg}
 \end{frame}
 
 \begin{frame}{Bioinformatics Training Lab}
+\includegraphics[width=\textwidth,height=0.8\textheight,keepaspectratio]{photos/IMG_0199.jpg}
 \end{frame}
 
 \section{Tracks}
 
 \begin{frame}{People}
+\includegraphics[width=\textwidth,height=0.8\textheight,keepaspectratio]{photos/IMG_0165.jpg}
 \end{frame}
 
 \begin{frame}{Tracks}
+\begin{itemize}
+\item Stream A: Illumina array (QC,calling, SNP QC)
+\item Stream B: WGS/Exosome data (processing, QC, variant calling)
+\item Stream C: 16S rRNA analyses, data QC, chimera detection, OTU picking
+\item Stream D: Imputation and phasing
+\end{itemize}
 \end{frame}
 
 \section{Results}
 
-\begin{frame}{CWL Pipelines}
+\begin{frame}{Results}
+\begin{itemize}
+\item CWL and Nextflow based workflows for each of the streams
+\item Docker containers which contain all of the software required to
+  implement the workflows
+\item scripts using nova and cloud init to bring up cloud resources
+\end{itemize}
 \end{frame}
 
-\begin{frame}{Imputation Workflow}
+\section{Technology}
+\begin{frame}{Nextflow}
+\begin{itemize}
+\item Groovy-based
+\item Can call docker to run programs
+\item Channel infrastructure to connect different components of the
+  workflow
+\item Language is a bit clunky and has lots of boilerplate
+\end{itemize}
 \end{frame}
 
-\begin{frame}{Nova cloud-init structure}
+\begin{frame}{Open Stack}
+\begin{itemize}
+\item Open source cloud infrastructure
+\item Implementation at NCSA
+\item Provision using cloud-init and nova from the command line
+\item cloud-init is present in most Debian and Ubuntu cloud images
+\end{itemize}
 \end{frame}
 
+\begin{frame}{Docker}
+\begin{itemize}
+\item Containers to isolate what is running from the host operating system
+\item docker images which contain the actual code to run
+\item Docker file which describes how to build the images
+\end{itemize}
+\end{frame}
+
+\begin{frame}[fragile]{Docker file}
+\footnotesize
+\begin{verbatim}
+FROM ubuntu:latest
+MAINTAINER Don Armstrong <don@donarmstrong.com>
+# Install wget
+RUN apt-get update && apt-get install -y wget && \
+    apt-get clean && \
+    rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*
+RUN wget \
+ http://mathgen.stats.ox.ac.uk/impute/impute_v2.3.2_x86_64_static.tgz && \
+ tar -zxvf impute_v2.3.2_x86_64_static.tgz && \
+ mv impute_v2.3.2_x86_64_static/impute2 /usr/bin/impute2 && \
+ mkdir /opt/impute2/example -p && \
+ mv impute_v2.3.2_x86_64_static/Example/* \
+              /opt/impute2/example && \
+ rm -rf impute_v2.3.2_x86_64_static \
+ impute_v2.3.2_x86_64_static.tgz
+\end{verbatim}
+\end{frame}
 \end{document}
-- 
2.39.2