Skip to content

Git course
Git course
Commit 756874cc authored by Jeroen F.J. Laros's avatar Jeroen F.J. Laros
Browse files
Options

Updated the skeleton lecture and handouts.

parent d42938da
Hide whitespace changes
Inline Side-by-side
Showing with 107 additions and 37 deletions
skeleton/markdown.html 0 → 100644
View file @ 756874cc
<!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>
skeleton/skeleton.tex
View file @ 756874cc
......@@ -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
......
skeleton/skeleton_handouts.tex
View file @ 756874cc
......@@ -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.
......
Markdown is supported
0% or
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment