\documentclass[english,serif,mathserif,xcolor=pdftex,dvipsnames,table]{beamer}
\usepackage{lsci}

\title[AppPot]{%
  Introduction to AppPot, I
}
\author[R. Murri]{%
  \textbf{Riccardo Murri} \\
  Grid Computing Competence Center, \\
  Organisch-Chemisches Institut, \\
  University of Zurich
}
\date{Dec.~8,~2011}

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\begin{document}

% title frame
\maketitle


\section{Introduction}

\begin{frame}
  \frametitle{Today's class}
  
  An introduction to the AppPot VM,
  and a little hands-on experience.

  \+
  {\small These slides are available for download from: 
    \url{http://www.gc3.uzh.ch/teaching/lsci2011/lab11.pdf}}
\end{frame}


\begin{frame}
  \frametitle{Quickstart, I}
  \emph{1.} Add the GC3 software repository as an APT source.
  
  \+ Download
  {\small\url{http://www.gc3.uzh.ch/teaching/lsci2011/lab11/gc3.list}} and
  move it to \texttt{/etc/apt/sources.list.d/gc3.list}

  \+
  \emph{2.} Run \texttt{sudo apt-get update} to pull the new package
  descriptions. 
\end{frame}

\begin{frame}[fragile]
  \frametitle{Quickstart, II}
  \emph{3.} Install the \texttt{apppot-start} package:
\begin{semiverbatim}
\$ {sudo apt-get install} \textbf{apppot-start}
\end{semiverbatim}

  \+
  \textbf{Note:} there's also an \texttt{apppot} package, that you
  should \textbf{not} install, as it transforms your boot sequence into
  the one used by the AppPot VM.
\end{frame}

\begin{frame}[fragile]
  \frametitle{Quickstart, III}
  \emph{4.} Download the AppPot VM disk image from:
  {\small\url{http://www.gc3.uzh.ch/download/apppot/apppot0.25.disk.img}}

  \+
  {\em (That's a 2GB download, so if you have questions now is a good
    time to ask.)}

  \+
  \emph{5.} Start it using the command:
\begin{semiverbatim}
\$ \textbf{apppot-start} --apppot apppot0.25.disk.img
\end{semiverbatim}
\end{frame}


\begin{frame}
  \frametitle{The AppPot console}
  There's only one console in AppPot, and no graphics.

  \+
  But the only console runs \href{http://www.gnu.org/s/screen/}{GNU
    \texttt{screen}}, so you can use it to get more shells.

  \+
  All \texttt{screen} commands use \textsl{\color{uzh@blue} Ctrl+A} as a prefix,
  followed~by:
  \begin{description}
  \item[c] for starting a new \textbf{c}onsole
  \item[n] for switching to the \textbf{n}ext console
  \item[p] for switching to the \textbf{p}revious console
  \item[?] for getting on-screen help
  \end{description}
\end{frame}


\begin{frame}[fragile]
  \frametitle{System administration in AppPot}
  There's only one user account, named \texttt{user}.

  \+
  This account has unrestricted password-less \texttt{sudo} access. 

  \+
  So you can use it to run administrative commands, 
  for~example:
\begin{semiverbatim}
\$ \textbf{sudo} apt-get clean
\end{semiverbatim}
\end{frame}


\section{Selectome on AppPot}

\begin{frame}[fragile]
  \frametitle{Installing the CODEML application}
  We're going to install the CODEML application in your AppPot VM,
  needed for the
  \href{http://wiki.isb-sib.ch/grid-selectome/Codeml_Requirements_Form#Application_and_Project_Description}{Grid-Selectome}
  exercise project.

  \+
  \begin{exercise}
    Follow the installation instructions at {\small
      \url{http://wiki.isb-sib.ch/grid-selectome/Codeml_Requirements_Form#Installation_instructions}}
    and install \texttt{CODEML}.  (It might be necessary to install
    software using \texttt{sudo apt-get}.)

    \+
    Verify that installation works with the instructions given in the
    ``Installation validation test'' section.

    \+
    Can you write a script to automate the validation/verification?
  \end{exercise}
\end{frame}

\section{The End}

\begin{frame}
  \frametitle{More stuff}
  \begin{center}
    AppPot home page: \href{http://AppPot.googlecode.com}{http://AppPot.googlecode.com}

    \+
    Source code: \texttt{svn co http://AppPot.googlecode.com/svn}
    
    \+
    e-mail: \texttt{riccardo.murri@gmail.com}, \texttt{sergio.maffioletti@gc3.uzh.ch}
  \end{center}
\end{frame}


\end{document}

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