Added short presentation.

.gitmodules

+[submodule ".submodules/presentation"]
+	path = .submodules/presentation
+	url = https://git.lumc.nl/j.f.j.laros/presentation.git

presentation @ 2381b425

+Subproject commit 2381b4253b21edf0444e34fd8a8044e81142e40e

presentations/cookiecutter/Makefile

+../../.submodules/presentation/Makefile
\ No newline at end of file

presentations/cookiecutter/beamerthemelumc.sty

+../../.submodules/presentation/beamerthemelumc.sty
\ No newline at end of file

presentations/cookiecutter/cookiecutter.tex

+\documentclass[slidestop]{beamer}
+
+\author{Jeroen F.J. Laros}
+\title{Cookiecutter}
+\providecommand{\mySubTitle}{}
+\providecommand{\myConference}{NGS work discussion}
+\providecommand{\myDate}{21-09-2016}
+\providecommand{\myGroup}{}
+\providecommand{\myDepartment}{Department of Human Genetics}
+\providecommand{\myCenter}{Center for Human and Clinical Genetics}
+
+\usetheme{lumc}
+
+\begin{document}
+
+% This disables the \pause command, handy in the editing phase.
+%\renewcommand{\pause}{}
+
+% Make the title slide.
+\makeTitleSlide{\includegraphics[height=3.5cm]{cookiecutter}}
+
+% First page of the presentation.
+\section{Introduction}
+\makeTableOfContents
+
+\subsection{Project template}
+\begin{pframe}
+  Common structure for all projects.
+  \begin{itemize}
+    \item Directory structure (\lstinline{analysis}, \lstinline{data},
+      \lstinline{doc} and \lstinline{src}).
+    \item A top level \lstinline{README.md} and one in every directory.
+  \end{itemize}
+  \bigskip
+
+  After initialising the template:
+  \begin{itemize}
+    \item Fill in the details in the README files.
+    \item Add a new project on our GitLab server.
+    \item Set the remote to the newly created project.
+  \end{itemize}
+  \vfill
+
+  \permfoot{\url{https://git.lumc.nl/sasc/project\_template}}
+\end{pframe}
+
+\begin{pframe}
+  \begin{lstlisting}[caption={Usage example.}]
+    {project name}
+    ==============
+
+
+    * Owner    : {owner email}
+
+    * Analyst  : {sasc analyst email}
+
+    * Reviewer : {sasc reviewer email}
+  \end{lstlisting}
+  \bigskip
+
+  This is not exactly what we had in mind.
+\end{pframe}
+
+\section{Cookiecutter}
+\subsection{Better project templates}
+\begin{pframe}
+  How to use:
+  \begin{itemize}
+    \item Answer a number of questions.
+    \item Everything else is done automatically.
+  \end{itemize}
+  \bigskip
+
+  Features:
+  \begin{itemize}
+    \item Jinja2 \emph{variables} can be used in directory names, file names
+      and content.
+    \item Macros for commonly used functions.
+    \item Pre- and post-generate hooks.
+    \item Configurable default values (your own name, e-mail, etc.).
+  \end{itemize}
+  \vfill
+
+  \permfoot{\url{https://cookiecutter.readthedocs.io}}
+\end{pframe}
+
+\subsection{Starting a project}
+\begin{pframe}
+  \begin{minipage}{\textwidth}
+    \begin{lstlisting}[caption={Starting a project.}]
+      full_name [Jeroen F.J. Laros]: 
+      email [J.F.J.Laros@lumc.nl]: 
+      client_full_name [John Doe]: Johann Gambolputty
+      client_email [J.Gambolputty@lumc.nl]: 
+      client_username [j.gambolputty]: 
+      sequencing_centre [LGTC]: GenomeScan
+      sequencing_platform [Illumina HiSeq 2500]:
+      experiment_type [RNASeq]: Exome
+      project_number [1]: 999
+      project_name [project-999-exome-jgambolputty]: 
+      gitlab_repo_namespace [sasc]: 
+    \end{lstlisting}
+  \end{minipage}
+  \vfill
+
+  \permfoot{\url{https://git.lumc.nl/sasc/project-999-exome-jgambolputty}}
+\end{pframe}
+
+\begin{pframe}
+  What just happened:
+  \begin{itemize}
+    \item A new Git repository was created.
+    \item The repository was populated with items from the template.
+    \item The template was filled in using the provided answers.
+    \item A project was created on our GitLab server.
+    \item The client was added to the project (received an e-mail).
+  \end{itemize}
+  \vfill
+
+  \permfoot{\url{https://git.lumc.nl/sasc/cookiecutter-data-analysis}}
+\end{pframe}
+
+% Make the acknowledgements slide.
+\makeAcknowledgementsSlide{
+  \begin{tabular}{l}
+    Wibowo Arindrarto
+  \end{tabular}
+}
+
+\end{document}

presentations/cookiecutter/logos

+../../.submodules/presentation/logos
\ No newline at end of file