add h3africa slides

diff --git a/.gitignore b/.gitignore
new file mode 100644 (file)
index 0000000..5888e22
--- /dev/null
+++ b/.gitignore
@@ -0,0 +1,19 @@
+cache
+auto
+figure
+*.aux
+*.bbl
+*.bcf
+*.blg
+*.fdb_latexmk
+*.fls
+*.log
+*.out
+*.pdf
+*.run.xml
+*.tex
+*.lof
+*.lot
+*.toc
+*.nav
+*.snm
\ No newline at end of file

diff --git a/Makefile b/Makefile
new file mode 100644 (file)
index 0000000..4eb9ade
--- /dev/null
+++ b/Makefile
@@ -0,0 +1,17 @@
+R ?= R
+
+all: h3abionet_hackathon.pdf
+
+%.pdf: %.svg
+       inkscape -A $@ $<
+       pdfcrop $@
+       mv $(dir $@)*-crop.pdf $@
+
+%.png: %.svg
+       inkscape -e $@ -d 300 $<
+
+%.tex: %.Rnw
+       $(R) --encoding=utf-8 -e "library('knitr'); knit('$<')"
+
+%.pdf: %.tex $(wildcard *.bib) $(wildcard *.tex)
+       latexmk -pdf -pdflatex='xelatex -interaction=nonstopmode %O %S' -bibtex -use-make $<

diff --git a/figures/.gitignore b/figures/.gitignore
new file mode 100644 (file)
index 0000000..39d6bc2
--- /dev/null
+++ b/figures/.gitignore
@@ -0,0 +1,5 @@
+igb_wordmark.pdf
+igb_wordmarks.zip
+uofi_mark.pdf
+uofi_mark.zip
+relevant_xkcd.png

diff --git a/figures/Makefile b/figures/Makefile
new file mode 100644 (file)
index 0000000..f4b2c49
--- /dev/null
+++ b/figures/Makefile
@@ -0,0 +1,22 @@
+#!/usr/bin/make -f
+
+all: uofi_mark.pdf igb_wordmark.pdf
+
+igb_wordmarks.zip: 
+       wget -O $@ "http://www.igb.illinois.edu/sites/default/files/upload/Wordmarks-Eps.zip"
+
+igb_wordmark.pdf: igb_wordmarks.zip
+       unzip igb_wordmarks.zip Wordmark-black-tag-outlines.eps
+       epstopdf --outfile=$@ Wordmark-black-tag-outlines.eps
+       rm -f Wordmark-black-tag-outlines.eps
+
+uofi_mark.zip: 
+       wget -O $@ "http://identitystandards.illinois.edu/assets/logos/uclogo_1867_horz_bold.zip"
+
+uofi_mark.pdf: uofi_mark.zip
+       unzip uofi_mark.zip uclogo_1867_horz_bold/pc/uclogo_1867_horz_bold.eps
+       epstopdf --outfile=$@ uclogo_1867_horz_bold/pc/uclogo_1867_horz_bold.eps
+       rm -rf uclogo_1867_horz_bold
+
+relevant_xkcd.png:
+       wget -O $@ "http://imgs.xkcd.com/comics/cells.png"

diff --git a/h3abionet_hackathon.Rnw b/h3abionet_hackathon.Rnw
new file mode 100644 (file)
index 0000000..ffc730e
--- /dev/null
+++ b/h3abionet_hackathon.Rnw
@@ -0,0 +1,105 @@
+\documentclass[ignorenonframetext]{beamer}
+\usepackage{fontspec}
+\setmainfont{FreeSerif}
+\setsansfont{FreeSans}
+\setmonofont{FreeMono}
+\usepackage{url}
+\usepackage{fancyhdr}
+\usepackage{graphicx}
+\usepackage[bf]{caption}
+\usepackage{rotating}
+\usepackage{wrapfig}
+\usepackage{fancybox}
+\usepackage{booktabs}
+% \usepackage{multirow}
+\usepackage{acronym}
+\usepackage{qrcode}
+\usepackage[backend=biber,natbib=true,hyperref=true,style=nature]{biblatex}
+\addbibresource{references.bib}
+% \usepackage[nomargin,inline,draft]{fixme}
+% \newcommand{\DLA}[1]{\textcolor{red}{\fxnote{DLA: #1}}}
+% \usepackage[hyperfigures,bookmarks,colorlinks,citecolor=black,filecolor=black,linkcolor=black,urlcolor=black]{hyperref}
+\usepackage{texshade}
+\usepackage{tikz}
+\usepackage{nameref}
+\usepackage{zref-xr,zref-user}
+\renewcommand*{\bibfont}{\tiny}
+
+% The textpos package is necessary to position textblocks at arbitary 
+% places on the page.  Use showboxes option to show outlines of textboxes.
+% \usepackage[absolute]{textpos}
+\usepackage[absolute,showboxes]{textpos}
+
+\usepackage{multirow}
+\usepackage{array}
+
+\mode<presentation>{ 
+  \usetheme{CambridgeUS}
+  % http://identitystandards.illinois.edu/graphicstandardsmanual/generalguidelines/colors.html
+  \definecolor{ilboldblue}{HTML}{002058}
+  \definecolor{ilboldorange}{HTML}{E87722}
+  \definecolor{ilblue}{HTML}{606EB2}
+  \definecolor{ilorange}{HTML}{D45D00}
+  \setbeamercolor{alerted text}{fg=ilboldorange}
+  \setbeamercolor*{palette primary}{fg=ilblue,bg=ilorange}
+  \setbeamercolor*{palette secondary}{fg=ilblue!20!white,bg=ilorange}
+  \setbeamercolor*{palette tertiary}{bg=ilblue,fg=ilorange}
+  \setbeamercolor*{palette quaternary}{fg=ilblue,bg=ilorange}
+  
+  \setbeamercolor*{sidebar}{fg=ilorange,bg=ilboldblue}
+  
+  \setbeamercolor*{palette sidebar primary}{fg=ilblue!10!white,bg=ilorange}
+  \setbeamercolor*{palette sidebar secondary}{fg=ilorange}
+  \setbeamercolor*{palette sidebar tertiary}{fg=ilblue}
+  \setbeamercolor*{palette sidebar quaternary}{fg=ilorange}
+  
+  % \setbeamercolor*{titlelike}{parent=palette primary}
+  \setbeamercolor{titlelike}{parent=palette primary,fg=ilboldblue,bg=ilorange}
+  \setbeamercolor{frametitle}{fg=ilboldorange,bg=ilblue!80!white}
+  \setbeamercolor{frametitle right}{fg=ilboldblue,bg=ilorange}
+  
+  \setbeamercolor*{separation line}{}
+  \setbeamercolor*{fine separation line}{}
+  \setbeamercovered{transparent}  
+  \logo{\begin{tikzpicture}% Pale figure
+      {\node[opacity=0.5]{\IfFileExists{figures/igb_wordmark.pdf}{\includegraphics[width=2cm,height=0.5cm,keepaspectratio]{figures/igb_wordmark}}{}%
+        };}%
+    \end{tikzpicture}}
+}
+
+\title[H3ABionet Hackathon]{H3ABionet Hackathon in Pretoria, South Africa}
+\author{Don L. Armstrong}
+\institute[IGB]{Institute for Genomic Biology, University of Illinois, Urbana-Champaign}
+
+\begin{document}
+
+\frame[plain]{\titlepage}
+
+\section{Location}
+
+\begin{frame}{Pretoria}
+\end{frame}
+
+\begin{frame}{Bioinformatics Training Lab}
+\end{frame}
+
+\section{Tracks}
+
+\begin{frame}{People}
+\end{frame}
+
+\begin{frame}{Tracks}
+\end{frame}
+
+\section{Results}
+
+\begin{frame}{CWL Pipelines}
+\end{frame}
+
+\begin{frame}{Imputation Workflow}
+\end{frame}
+
+\begin{frame}{Nova cloud-init structure}
+\end{frame}
+
+\end{document}