using_make_for_science.Rnw

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  11 \usepackage{booktabs}
  12 \usepackage{threeparttable}
  13 \usepackage[backend=biber,natbib=true,hyperref=true,style=numeric-comp]{biblatex}
  14 \bibliography{references}
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  76 }
  77
  78 \title{Using make for science}
  79
  80 \author{Don Armstrong}
  81 \date{\today}
  82 \subject{make for science}
  83 \begin{document}
  84
  85 \frame[plain]{\titlepage}
  86
  87 \mode<article>{\maketitle}
  88
  89 \section{What make was made for}
  90 \begin{frame}{What was make originally made to do?}
  91   \begin{itemize}
  92   \item Compiling and installing software from source
  93   \item Replacement of operating system specific compilation and
  94     installation shell scripts
  95   \item Re-compile when dependencies of the software were modified
  96   \end{itemize}
  97 \end{frame}
  98
  99 \subsection{Brief history of makes}
 100
 101 \begin{frame}{Brief history of make-alikes}
 102   \begin{itemize}
 103   \item
 104     \href{http://pubs.opengroup.org/onlinepubs/009695399/utilities/make.html}{POSIX
 105       Make} (standardization of basic features of make)
 106   \item \href{http://www.gnu.org/software/make/manual/}{GNU Make}
 107     (standard make on Linux and OS X)
 108   \item \href{https://www.freebsd.org/cgi/man.cgi?query=make(1)}{BSD
 109       Make} (pmake or bmake)
 110   \item
 111     \href{https://msdn.microsoft.com/en-us/library/dd9y37ha.aspx}{nmake}
 112     (Part of visual studio)
 113   \item \href{http://plan9.bell-labs.com/sys/doc/mk.html}{Mk} (Plan 9
 114     replacement of make)
 115   \end{itemize}
 116 \end{frame}
 117
 118 \subsection{Other solutions in this problem space}
 119
 120 \begin{frame}{Other non-make dependency builders}
 121   \begin{itemize}
 122   \item Ant (popular for java software)
 123   \item Cabal (popular for Haskell)
 124   \item Maven (also java)
 125   \item Rake (ruby build took)
 126   \item Gradle (Rake DSL)
 127   \item Leiningen (Clojure)
 128   \item Tweaker (task definitions in any language)
 129   \item
 130     \href{https://en.wikipedia.org/wiki/List_of_build_automation_software}{Wikipedia
 131       List of build automation software}
 132   \end{itemize}
 133 \end{frame}
 134
 135 \section{Introduction to Makefiles}
 136
 137 \section{Examples}
 138
 139 \subsection{This Presentation}
 140
 141 \subsection{Can you dig it?}
 142
 143 \subsection{Calling records from SRA}
 144
 145 \section{Why not make?}
 146
 147 \subsection{Timestamps}
 148
 149 \subsection{Complicated Workflows}
 150
 151 \section{Further Resources}
 152
 153
 154 \end{document}