using_make_for_science.Rnw

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  79
  80 \title{Using make for science}
  81
  82 \author{Don Armstrong}
  83 \date{\today}
  84 \subject{make for science}
  85 \begin{document}
  86
  87 \frame[plain]{\titlepage}
  88
  89 \mode<article>{\maketitle}
  90
  91 \section{What make was made for}
  92 \begin{frame}{What was make originally made to do?}
  93   \begin{itemize}
  94   \item Compiling and installing software from source
  95   \item Replacement of operating system specific compilation and
  96     installation shell scripts
  97   \item Re-compile when dependencies of the software were modified
  98   \end{itemize}
  99 \end{frame}
 100
 101 \subsection{Brief history of makes}
 102
 103 \begin{frame}{Brief history of make-alikes}
 104   \begin{itemize}
 105   \item
 106     \href{http://pubs.opengroup.org/onlinepubs/009695399/utilities/make.html}{POSIX
 107       Make} (standardization of basic features of make)
 108   \item \href{http://www.gnu.org/software/make/manual/}{GNU Make}
 109     (standard make on Linux and OS X)
 110   \item \href{https://www.freebsd.org/cgi/man.cgi?query=make(1)}{BSD
 111       Make} (pmake or bmake)
 112   \item
 113     \href{https://msdn.microsoft.com/en-us/library/dd9y37ha.aspx}{nmake}
 114     (Part of visual studio)
 115   \item \href{http://plan9.bell-labs.com/sys/doc/mk.html}{Mk} (Plan 9
 116     replacement of make)
 117   \end{itemize}
 118 \end{frame}
 119
 120 \subsection{Other solutions in this problem space}
 121
 122 \begin{frame}{Other non-make dependency builders}
 123   \begin{itemize}
 124   \item Ant (popular for java software)
 125   \item Cabal (popular for Haskell)
 126   \item Maven (also java)
 127   \item Rake (ruby build took)
 128   \item Gradle (Rake DSL)
 129   \item Leiningen (Clojure)
 130   \item Tweaker (task definitions in any language)
 131   \item
 132     \href{https://en.wikipedia.org/wiki/List_of_build_automation_software}{Wikipedia
 133       List of build automation software}
 134   \end{itemize}
 135 \end{frame}
 136
 137 \section{Introduction to Makefiles}
 138
 139 \begin{frame}[fragile]{Simple Makefile}
 140 \begin{minted}[showtabs]{make}
 141 hello_world:
 142         echo "hello world" > hello_world
 143 \end{minted}
 144 \end{frame}
 145
 146 \subsection{General Syntax}
 147
 148
 149 \begin{frame}[fragile]{Simple Makefile}
 150 \begin{minted}[showtabs]{make}
 151 hello_world:
 152         echo "hello world" > hello_world
 153 \end{minted}
 154 \end{frame}
 155
 156 \subsection{Variables}
 157
 158 \subsection{Rules}
 159
 160 \subsubsection{Default Target}
 161
 162 \subsubsection{Special Targets}
 163
 164 \subsubsection{Pattern Rules}
 165
 166 \subsection{Functions}
 167
 168
 169 \section{Examples}
 170
 171 \subsection{This Presentation}
 172
 173 \subsection{Can you dig it?}
 174
 175 \subsection{Calling records from SRA}
 176
 177 \section{Why not make?}
 178
 179 \subsection{Timestamps}
 180
 181 \subsection{Complicated Workflows}
 182
 183 \section{Further Resources}
 184
 185
 186 \end{document}