Updated the skeleton presentation, added handouts.

skeleton/skeleton.tex

 \documentclass[slidestop]{beamer}
 
-\title{Introduction to Version Control}
+\title{Analysis projects skeleton}
 \providecommand{\myConference}{Git course}
 \providecommand{\myDate}{Monday, October 14, 2013}
 \author{Jeroen F. J. Laros}
@@ -32,12 +32,263 @@
 % First page of the presentation.
 \section{Introduction}
 \begin{frame}
-  \frametitle{}
+  \frametitle{Shared projects.}
+
+  Most of us work on multiple projects with multiple people.
+  \bigskip
+
+  That is why is is convenient to:
+  \begin{itemize}
+    \item Have everything in one place.
+    \begin{itemize}
+      \item Data.
+      \item Code.
+      \item Documentation.
+    \end{itemize}
+    \item Have the same structure for all projects.
+  \end{itemize}
+\end{frame}
+
+\begin{frame}
+  \frametitle{Project skeleton.}
+
+  That is why we made a \emph{skeleton} project.
+  \bigskip
+
+  Usage:
+  \begin{itemize}
+    \item Make a \emph{fork} (copy) of the skeleton project.
+    \item Rename the project.
+    \item Do a checkout.
+    \item Start working with it.
+  \end{itemize}
+\end{frame}
+
+\section{Starting a project}
+\begin{fframe}
+  \frametitle{Forking}
+
+  Make a new analysis project.
+  \begin{itemize}
+    \item Go to the ``Project skeleton'' project page on our GitLab server.
+    \item Click ``Fork'' to fork it to a new project.
+    \item Go to ``Settings'' to rename the new project.
+    \begin{itemize}
+      \item Change both the project as well as the repository path.
+    \end{itemize}
+  \end{itemize}
+  
+  \vfill
+  \permfoot{https://git.lumc.nl/lgtc-bioinformatics/project-skeleton}
+\end{fframe}
+
+\begin{frame}
+  \frametitle{Configuration}
+
+  Configure your project.
+  \begin{itemize}
+    \item Choose to make your project public or not.
+    \begin{itemize}
+      \item Public by default.
+      \item Public really means public.
+    \end{itemize}
+    \item Add the people that work on this project.
+  \end{itemize}
+\end{frame}
+
+\section{Project structure}
+\begin{frame}
+  \frametitle{Global overview.}
+
+  Project layout:
+  \begin{itemize}
+    \item analysis
+    \item data
+    \item doc
+    \item src
+  \end{itemize}
+  \bigskip
+
+  Ideally, every directory in the project has a \bt{README} file.
+\end{frame}
+
+\begin{frame}
+  \frametitle{The toplevel \bt{\,README\,\,} file.}
+
+  This file contains general information about the project, for example:
+  \begin{itemize}
+    \item Who leads the project.
+    \item Who participates in the project.
+    \item The amount of hours people have spent on this project.
+  \end{itemize}
+\end{frame}
+
+\begin{frame}
+  \frametitle{The \bt{\,doc\,\,} directory.}
+
+  Documentation on the project:
+  \begin{itemize}
+    \item Annotated sample lists.
+    \item Goal of the project.
+    \item Related work and literature.
+    \begin{itemize}
+      \item You may want to note who provided the documentation.
+    \end{itemize}
+  \end{itemize}
+\end{frame}
+
+\begin{frame}
+  \frametitle{The \bt{\,data\,\,} directory.}
+
+  Used to store all raw data.
+  \bigskip
+
+  The \bt{README} contains:
+  \begin{itemize}
+    \item Description of the delivered data.
+    \begin{itemize}
+      \item Sequencing centre.
+      \item Platform.
+      \item Molecular type.
+      \item Owner.
+      \item Gatherer.
+    \end{itemize}
+    \item Description of other data.
+    \begin{itemize}
+      \item Perhaps you already got BAM files.
+      \begin{itemize}
+        \item Who aligned it?
+        \item Which aligner?
+      \end{itemize}
+    \end{itemize}
+  \end{itemize}
+
+\end{frame}
+
+\begin{frame}
+  \frametitle{The \bt{\,analysis\,\,} directory.}
+
+  All analysis related files are stored here:
+  \begin{itemize}
+    \item Run scripts.
+    \item Make files.
+    \item Result files.
+  \end{itemize}
+  \bigskip
+
+  Try to separate self-contained parts of the analysis in their own
+  subdirectories and document dependencies in a \bt{README} file.
+  \begin{itemize}
+    \item Normal data analysis.
+    \item $k$-mer analysis.
+  \end{itemize}
+\end{frame}
+
+\begin{frame}
+  \frametitle{The \bt{\,src\,\,} directory.}
+
+  Any custom scripts and specific software versions for this project.
+  \bigskip
+
+  When these scripts are useful for other projects, move them to their own
+  repository.
+\end{frame}
+
+\section{Working with large files}
+\begin{fframe}
+  \frametitle{Git is not designed for massive files.}
+
+  Some problems with large files:
+  \begin{itemize}
+    \item Limited storage on the server.
+    \item Checking out a repository would take a long time.
+  \end{itemize}
+  \bigskip
+
+  We do want to have some way to track our input and output data. This can be
+  done with \bt{git-annex}.
+
+  \vfill
+  \permfoot{http://git-annex.branchable.com/}
+\end{fframe}
+
+\begin{frame}[fragile]
+  \frametitle{Git annex.}
+
+  \begin{itemize}
+    \item Manage large files without storing them.
+    \item Store file checksums.
+    \item Prevent files from being deleted accidentally.
+  \end{itemize}
+  \bigskip
+  \pause
+
+  You first have to enable this for your repository.
+
+  \begin{lstlisting}[language=none, caption=Enable git-annex.]
+    $ git annex init "<name>"
+  \end{lstlisting}
+\end{frame}
+
+\begin{frame}[fragile]
+  \frametitle{Adding big files.}
+
+  \begin{lstlisting}[language=none, caption=Adding files.]
+    $ git annex add <filename>
+    $ git commit
+  \end{lstlisting}
+  \bigskip
+
+  In a clone, this file will visible, but not really present.
+  \begin{lstlisting}[language=none, caption=Make a file available.]
+    $ file <filename>
+    <filename>: broken symbolic link to ...
+    $ git annex get <filename>
+  \end{lstlisting}
+\end{frame}
+
+\begin{frame}[fragile]
+  \frametitle{Removing files.}
+
+  As long as there are enough copies available, you can remove files.
+  \begin{lstlisting}[language=none, caption=A failing drop command.]
+    $ git annex drop <filename>
+    drop bigfile (unsafe)
+    git-annex: drop: 1 failed
+  \end{lstlisting}
+  \bigskip
+
+  It is actually quite well protected.
+  \begin{lstlisting}[language=none, caption=rm fails too.]
+    $ rm -rf <repository>
+    rm: cannot remove <repository>/.git/annex/objects/...
+  \end{lstlisting}
+\end{frame}
+
+\begin{frame}[fragile]
+  \frametitle{Sync your results.}
+
+  Let the other repositories know what you have done.
+  \begin{lstlisting}[language=none, caption=.]
+    $ git annex sync
+  \end{lstlisting}
+\end{frame}
+
+\begin{frame}[fragile]
+  \frametitle{Working together on the same clone.}
+ 
+ If you need to work with other people on the same repository clone on the
+ Shark cluster, you can use the following command to give group access:
+ 
+  \begin{lstlisting}[language=none, caption=.]
+    $ find -type d -exec chmod 775 {} \;
+    $ find -type f -exec chmod 664 {} \;
+  \end{lstlisting}
 \end{frame}
 
 \section{Questions?}
 \lastpagetemplate
-\begin{frame}
+\begin{fframe}
   \begin{center}
     Acknowledgements:
     \bigskip
@@ -48,6 +299,10 @@
     Zuotian Tatum
 
   \end{center}
-\end{frame}
+
+  \vfill
+  \permfoot{http://git-annex.branchable.com/}
+  \permfoot{https://git.lumc.nl/lgtc-bioinformatics/project-skeleton}
+\end{fframe}
 
 \end{document}

skeleton/skeleton_handouts.tex

+\documentclass{article}
+\usepackage{fullpage}
+\usepackage{listings}
+
+\frenchspacing
+\setlength{\parindent}{0pt}
+\pagestyle{empty}
+
+\begin{document}
+\begin{center}
+{\bf Git Introduction Course}
+
+Project skeleton practical.
+\end{center}
+\bigskip
+
+\subsubsection*{Git annex.}
+First, we make an empty repository:
+\begin{lstlisting}
+  $ mkdir annex_project
+  $ cd annex_project
+  $ git init
+  $ git annex init "Original repository."
+\end{lstlisting}
+\bigskip
+
+Now add a ``big file'' and annex it.
+\begin{lstlisting}
+  $ dd if=/dev/urandom of=bigfile.dat count=1024
+  $ git annex add bigfile.dat
+  $ git commit -m "Added big file."
+\end{lstlisting}
+\bigskip
+
+Now, we clone the project and let this repository know where the clone is.
+\begin{lstlisting}
+  $ git clone . ../annex_clone
+  $ git remote add annex_clone ../annex_clone
+  $ cd ../annex_clone
+  $ git annex init "Cloned repository."
+\end{lstlisting}
+\bigskip
+
+With the ``\texttt{file}'' command you can now see that
+``\texttt{bigdata.dat}'' is not present in this repository.
+\begin{lstlisting}
+  $ git pull
+  $ git annex get bigfile.dat
+\end{lstlisting}
+\bigskip
+
+You can now remove the big data file from the original repository.
+\begin{lstlisting}
+  $ cd ../annex_project
+  $ git annex drop bigfile.dat
+\end{lstlisting}
+
+But you can not remove it from the clone.
+
+\subsubsection*{Project skeleton.}
+Search for the ``Project skeleton''.
+\begin{itemize}
+  \item \emph{Hint:} Click the ``Public area'' icon and use the search option.
+\end{itemize}
+\bigskip
+
+Suppose you are going to do an RNASeq analysis. You have the following files:
+\begin{itemize}
+  \item read\_1.fq
+  \item read\_2.fq
+  \item Makefile
+\end{itemize}
+\end{document}