Merge branch 'jfjlaros_2014'

541cb890 · Laros · 14a508d8 · 48fd0fbf · 541cb890 · 541cb890
Commit 541cb890 authored 10 years ago by Laros
--- 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:

--- a/introduction/project_tree.xcf
+++ b/introduction/project_tree.xcf
--- a/skeleton/markdown.html
+++ b/skeleton/markdown.html
+<!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>
--- a/skeleton/markdown.xcf
+++ b/skeleton/markdown.xcf
--- 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

--- 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.