using_make_for_science.Rnw

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  14 \bibliography{references}
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  45
  46 \mode<presentation>{
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  49   \setbeamercovered{transparent}
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  53     \end{tikzpicture}}
  54 }
  55
  56 \title{Using make for science}
  57
  58 \author{Don Armstrong}
  59 \date{\today}
  60 \subject{make for science}
  61 \begin{document}
  62
  63 \frame[plain]{\titlepage}
  64
  65 \mode<article>{\maketitle}
  66
  67 \section{What make was made for}
  68 \begin{frame}{What was make originally made to do?}
  69   \begin{itemize}
  70   \item Compiling and installing software from source
  71   \item Replacement of operating system specific compilation and
  72     installation shell scripts
  73   \item Re-compile when dependencies of the software were modified
  74   \end{itemize}
  75 \end{frame}
  76
  77 \subsection{Brief history of makes}
  78
  79 \begin{frame}{Brief history of make-alikes}
  80   \begin{itemize}
  81   \item
  82     \href{http://pubs.opengroup.org/onlinepubs/009695399/utilities/make.html}{POSIX
  83       Make} (standardization of basic features of make)
  84   \item \href{http://www.gnu.org/software/make/manual/}{GNU Make}
  85     (standard make on Linux and OS X)
  86   \item \href{https://www.freebsd.org/cgi/man.cgi?query=make(1)}{BSD
  87       Make} (pmake or bmake)
  88   \item
  89     \href{https://msdn.microsoft.com/en-us/library/dd9y37ha.aspx}{nmake}
  90     (Part of visual studio)
  91   \item \href{http://plan9.bell-labs.com/sys/doc/mk.html}{Mk} (Plan 9
  92     replacement of make)
  93   \end{itemize}
  94 \end{frame}
  95
  96 \subsection{Other solutions in this problem space}
  97
  98 \begin{frame}{Other non-make dependency builders}
  99   \begin{itemize}
 100   \item Ant (popular for java software)
 101   \item Cabal (popular for Haskell)
 102   \item Maven (also java)
 103   \item Rake (ruby build took)
 104   \item Gradle (Rake DSL)
 105   \item Leiningen (Clojure)
 106   \item Tweaker (task definitions in any language)
 107   \item
 108     \href{https://en.wikipedia.org/wiki/List_of_build_automation_software}{Wikipedia
 109       List of build automation software}
 110   \end{itemize}
 111 \end{frame}
 112
 113 \section{Introduction to Makefiles}
 114
 115 \section{Examples}
 116
 117 \subsection{This Presentation}
 118
 119 \subsection{Can you dig it?}
 120
 121 \subsection{Calling records from SRA}
 122
 123 \section{Why not make?}
 124
 125 \subsection{Timestamps}
 126
 127 \subsection{Complicated Workflows}
 128
 129 \section{Further Resources}
 130
 131
 132 \end{document}