diff --git a/introduction/introduction.tex b/introduction/introduction.tex
index 4aacd0e625348ca39dc882408e783691a3848fe5..395c0504eb3f80dffbaefbceae4c64a9642628dd 100644
--- a/introduction/introduction.tex
+++ b/introduction/introduction.tex
@@ -49,6 +49,15 @@
\end{itemize}
\end{pframe}
+\begin{pframe}
+ \begin{figure}[]
+ \begin{center}
+ \includegraphics[height=0.85\textheight]{project_tree}
+ \end{center}
+ \caption{``I have my own system.''}
+ \end{figure}
+\end{pframe}
+
\subsection{Why should I use it?}
\begin{pframe}
For a single user:
diff --git a/introduction/project_tree.xcf b/introduction/project_tree.xcf
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diff --git a/skeleton/markdown.html b/skeleton/markdown.html
new file mode 100644
index 0000000000000000000000000000000000000000..f5e374d93a8ac445cb90a2345aa5bcd0fd022e3c
--- /dev/null
+++ b/skeleton/markdown.html
@@ -0,0 +1,28 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html xmlns="http://www.w3.org/1999/xhtml">
+<head>
+ <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
+ <meta http-equiv="Content-Style-Type" content="text/css" />
+ <meta name="generator" content="pandoc" />
+ <title></title>
+ <style>
+ div.padded {
+ padding-left: 30px;
+ padding-right: 30px;
+ }
+ </style>
+ <link href="https://git.lumc.nl/assets/application-9e18d69ef3096721155fd862af466f51.css" media="all" rel="stylesheet" />
+</head>
+<body>
+<div class="padded">
+ <h1 id="installation">Installation</h1>
+ <p>To install <a href="http://www.git-scm.com/">Git</a>:</p>
+ <pre><code>apt-get install git</code></pre>
+ <p>Now you can do the following:</p>
+ <ul>
+ <li>Make a new repository with <code>git init</code>.</li>
+ <li>Clone an existing repository with <code>git clone</code>.</li>
+ </ul>
+</div>
+</body>
+</html>
diff --git a/skeleton/markdown.xcf b/skeleton/markdown.xcf
new file mode 100644
index 0000000000000000000000000000000000000000..1b617117e9a0eea40e4e086de76f5051bf52604c
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diff --git a/skeleton/skeleton.tex b/skeleton/skeleton.tex
index 4e24a08f84350f97123d8e020209d3059bc89c51..65a4e3f9bd246b1e328da088bc3b3aa549998aab 100644
--- a/skeleton/skeleton.tex
+++ b/skeleton/skeleton.tex
@@ -54,10 +54,10 @@
\begin{pframe}
Usage:
\begin{itemize}
- \item Make a \emph{fork} (copy) of the skeleton project.
+ \item Make a clone of the skeleton project.
\item Rename the project.
- \item Clone your project.
- \item Start working with it.
+ \item Create a new project on the server.
+ \item Change the remote \bt{origin} to your new project.
\end{itemize}
\bigskip
\pause
@@ -76,35 +76,6 @@
\permfoot{https://git.lumc.nl/lgtc-bioinformatics/project-skeleton}
\end{pframe}
-%\subsection{Forking}
-%\begin{pframe}
-% 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{pframe}
-
-%\subsection{Configuration}
-%\begin{pframe}
-% 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{pframe}
-
\section{Project structure}
\subsection{Global overview}
\begin{pframe}
@@ -117,10 +88,35 @@
\end{itemize}
\bigskip
- Ideally, every directory in the project has a \bt{README} file.
+ Ideally, every directory in the project has a \bt{README.md} file.
+\end{pframe}
+
+\subsection{Markdown files}
+\begin{pframe}
+ \begin{lstlisting}[language=none, caption=Markdown snippet.]
+ # Installation
+
+ To install [Git](http://www.git-scm.com/):
+
+ apt-get install git
+
+ Now you can do the following:
+
+ - Make a new repository with `git init`.
+ - Clone an existing repository with `git clone`.
+ \end{lstlisting}
+\end{pframe}
+
+\begin{pframe}
+ \begin{figure}[]
+ \begin{center}
+ \includegraphics[width=\textwidth]{markdown}
+ \end{center}
+ \caption{Rendered markdown page.}
+ \end{figure}
\end{pframe}
-\subsection{The toplevel ``README'' file}
+\subsection{The toplevel ``README.md'' file}
\begin{pframe}
This file contains general information about the project, for example:
\begin{itemize}
@@ -148,7 +144,7 @@
Used to store all raw data.
\bigskip
- The \bt{README} contains:
+ The \bt{README.md} contains:
\begin{itemize}
\item Description of the delivered data.
\begin{itemize}
@@ -174,6 +170,7 @@
\begin{pframe}
All analysis related files are stored here:
\begin{itemize}
+ \item Symlinks to the actual data.
\item Run scripts.
\item Make files.
\item Result files.
@@ -181,7 +178,7 @@
\bigskip
Try to separate self-contained parts of the analysis in their own
- subdirectories and document dependencies in a \bt{README} file.
+ subdirectories and document dependencies in a \bt{README.md} file.
\begin{itemize}
\item Normal data analysis.
\item $k$-mer analysis.
@@ -263,6 +260,20 @@
\end{lstlisting}
\end{pframe}
+\subsection{Modifying files}
+\begin{pframe}
+ Sometimes we need to change the content of a file.
+ \bigskip
+
+ \begin{lstlisting}[language=none, caption=Unlocking a file.]
+ $ git annex edit <filename>
+ unlock <filename> (copying...) ok
+ \end{lstlisting}
+ \bigskip
+
+ You can use \bt{git annex add} when you are done.
+\end{pframe}
+
\subsection{Removing files}
\begin{pframe}
As long as there are enough copies available, you can remove files.
@@ -304,6 +315,29 @@
\end{lstlisting}
\end{pframe}
+\subsection{Cleaning your repository}
+\begin{pframe}
+ You can clean your repository with one command.
+ \bigskip
+
+ \begin{lstlisting}[language=none, caption=Remove untracked files.]
+ $ git clean -f -x
+ \end{lstlisting}
+
+ \begin{table}[]
+ \begin{center}
+ \begin{tabular}{ll}
+ option & description\\
+ \hline
+ \bt{-f} & Force (really remove).\\
+ \bt{-x} & Also remove \emph{ignored} files.\\
+ \bt{-n} & Do a \emph{dry run}.\\
+ \end{tabular}
+ \end{center}
+ \caption{Common options.}
+ \end{table}
+\end{pframe}
+
\subsection{Working together on the same clone}
\begin{pframe}
Sometimes you need to work with other people on the same repository clone.
@@ -331,8 +365,9 @@
Martijn Vermaat
- Zuotian Tatum
+ Wibowo Arindrarto
+ Zuotian Tatum
\end{center}
\vfill
diff --git a/skeleton/skeleton_handouts.tex b/skeleton/skeleton_handouts.tex
index e8cb27da8e92dcb0e1c3e9432fb2c7eeb249f8a4..e402b00dbe9d4e0d3f53235fea54fe8aa0795232 100644
--- a/skeleton/skeleton_handouts.tex
+++ b/skeleton/skeleton_handouts.tex
@@ -71,6 +71,13 @@ With the ``\texttt{file}'' command you can now see that
$ git pull
$ git annex get bigfile.dat
\end{lstlisting}
+
+\newpage
+
+Let the original repository know that you have a copy.
+\begin{lstlisting}
+ $ git annex sync
+\end{lstlisting}
\bigskip
You can now remove the big data file from the original repository.