h3abionet_hackathon.Rnw

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  69
  70 \title[H3ABionet Hackathon]{H3ABionet Hackathon in Pretoria, South Africa}
  71 \author{Don L. Armstrong}
  72 \institute[IGB]{Institute for Genomic Biology, University of Illinois, Urbana-Champaign}
  73
  74 \begin{document}
  75
  76 \frame[plain]{\titlepage}
  77
  78 \section{Location}
  79
  80 \begin{frame}{Pretoria}
  81 \includegraphics[width=\textwidth,keepaspectratio]{photos/pano.jpg}
  82 \end{frame}
  83
  84 \begin{frame}{Bioinformatics Training Lab}
  85 \includegraphics[width=\textwidth,height=0.8\textheight,keepaspectratio]{photos/IMG_0199.jpg}
  86 \end{frame}
  87
  88 \section{Tracks}
  89
  90 \begin{frame}{People}
  91 \includegraphics[width=\textwidth,height=0.8\textheight,keepaspectratio]{photos/IMG_0165.jpg}
  92 \end{frame}
  93
  94 \begin{frame}{Tracks}
  95 \begin{itemize}
  96 \item Stream A: Illumina array (QC,calling, SNP QC)
  97 \item Stream B: WGS/Exosome data (processing, QC, variant calling)
  98 \item Stream C: 16S rRNA analyses, data QC, chimera detection, OTU picking
  99 \item Stream D: Imputation and phasing
 100 \end{itemize}
 101 \end{frame}
 102
 103 \section{Results}
 104
 105 \begin{frame}{Results}
 106 \begin{itemize}
 107 \item CWL and Nextflow based workflows for each of the streams
 108 \item Docker containers which contain all of the software required to
 109   implement the workflows
 110 \item scripts using nova and cloud init to bring up cloud resources
 111 \end{itemize}
 112 \end{frame}
 113
 114 \section{Technology}
 115 \begin{frame}{Nextflow}
 116 \begin{itemize}
 117 \item Groovy-based
 118 \item Can call docker to run programs
 119 \item Channel infrastructure to connect different components of the
 120   workflow
 121 \item Language is a bit clunky and has lots of boilerplate
 122 \end{itemize}
 123 \end{frame}
 124
 125 \begin{frame}{Open Stack}
 126 \begin{itemize}
 127 \item Open source cloud infrastructure
 128 \item Implementation at NCSA
 129 \item Provision using cloud-init and nova from the command line
 130 \item cloud-init is present in most Debian and Ubuntu cloud images
 131 \end{itemize}
 132 \end{frame}
 133
 134 \begin{frame}{Docker}
 135 \begin{itemize}
 136 \item Containers to isolate what is running from the host operating system
 137 \item docker images which contain the actual code to run
 138 \item Docker file which describes how to build the images
 139 \end{itemize}
 140 \end{frame}
 141
 142 \begin{frame}[fragile]{Docker file}
 143 \footnotesize
 144 \begin{verbatim}
 145 FROM ubuntu:latest
 146 MAINTAINER Don Armstrong <don@donarmstrong.com>
 147 # Install wget
 148 RUN apt-get update && apt-get install -y wget && \
 149     apt-get clean && \
 150     rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*
 151 RUN wget \
 152  http://mathgen.stats.ox.ac.uk/impute/impute_v2.3.2_x86_64_static.tgz && \
 153  tar -zxvf impute_v2.3.2_x86_64_static.tgz && \
 154  mv impute_v2.3.2_x86_64_static/impute2 /usr/bin/impute2 && \
 155  mkdir /opt/impute2/example -p && \
 156  mv impute_v2.3.2_x86_64_static/Example/* \
 157               /opt/impute2/example && \
 158  rm -rf impute_v2.3.2_x86_64_static \
 159  impute_v2.3.2_x86_64_static.tgz
 160 \end{verbatim}
 161 \end{frame}
 162 \end{document}