Commit 756874cc authored by Jeroen F.J. Laros's avatar Jeroen F.J. Laros

Updated the skeleton lecture and handouts.

parent d42938da
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<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>
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......@@ -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
......
......@@ -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.
......
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