From 67ad0a4f2301587c569ef13b8b05087a9afbd05c Mon Sep 17 00:00:00 2001 From: Don Armstrong Date: Tue, 6 Sep 2016 07:53:10 -0700 Subject: [PATCH] add h3africa slides --- .gitignore | 19 ++++++++ Makefile | 17 +++++++ figures/.gitignore | 5 ++ figures/Makefile | 22 +++++++++ h3abionet_hackathon.Rnw | 105 ++++++++++++++++++++++++++++++++++++++++ 5 files changed, 168 insertions(+) create mode 100644 .gitignore create mode 100644 Makefile create mode 100644 figures/.gitignore create mode 100644 figures/Makefile create mode 100644 h3abionet_hackathon.Rnw diff --git a/.gitignore b/.gitignore new file mode 100644 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 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 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 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 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{ + \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} -- 2.39.2