Updated the skeleton presentation and handouts.

skeleton/skeleton.tex

@@ -50,41 +50,19 @@
   \end{itemize}
 \end{frame}
 
-\begin{frame}
+\section{Starting a project}
+\begin{fframe}
   \frametitle{Project skeleton.}
 
-  That is why we made a \emph{skeleton} project.
-  \bigskip
-
   Usage:
   \begin{itemize}
     \item Make a \emph{fork} (copy) of the skeleton project.
     \item Rename the project.
-    \item Do a checkout.
+    \item Clone your project.
     \item Start working with it.
   \end{itemize}
-\end{frame}
-
-\section{Starting a project}
-\begin{fframe}
-  \frametitle{Forking}
-
-  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{fframe}
-
-\begin{frame}
-  \frametitle{Configuration}
+  \bigskip
+  \pause
 
   Configure your project.
   \begin{itemize}
@@ -95,7 +73,41 @@
     \end{itemize}
     \item Add the people that work on this project.
   \end{itemize}
-\end{frame}
+
+  \vfill
+  \permfoot{https://git.lumc.nl/lgtc-bioinformatics/project-skeleton}
+\end{fframe}
+
+%\begin{fframe}
+%  \frametitle{Forking}
+%
+%  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{fframe}
+
+%\begin{frame}
+%  \frametitle{Configuration}
+%
+%  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{frame}
 
 \section{Project structure}
 \begin{frame}
@@ -129,7 +141,7 @@
 
   Documentation on the project:
   \begin{itemize}
-    \item Annotated sample lists.
+    \item Annotation of the data.
     \item Goal of the project.
     \item Related work and literature.
     \begin{itemize}
@@ -206,6 +218,14 @@
   \end{itemize}
   \bigskip
 
+  It also does not make much sense:
+  \begin{itemize}
+    \item These files are usually \emph{static}.
+    \item And probably \emph{binary}.
+  \end{itemize}
+  \bigskip
+  \pause
+
   We do want to have some way to track our input and output data. This can be
   done with \bt{git-annex}.
 

skeleton/skeleton_handouts.tex

@@ -14,7 +14,31 @@ Project skeleton practical.
 \end{center}
 \bigskip
 
+\subsubsection*{Project skeleton.}
+Search for the ``Project skeleton''.
+\begin{itemize}
+  \item \emph{Hint:} Click the ``Public area'' icon and use the search option.
+\end{itemize}
+\bigskip
+
+Follow the README to make your own analysis project.
+\bigskip
+
+Suppose you are going to do an RNASeq analysis. Retrieve the file
+``\texttt{data.tgz}'' from the
+wiki\footnote{https://humgenprojects.lumc.nl/trac/humgenprojects/wiki/git} and
+populate your analysis project.
+
 \subsubsection*{Git annex.}
+Check whether Git annex is installed, and install it if this is not the case.
+\begin{lstlisting}
+  $ git annex
+  git: 'annex' is not a git command. See 'git --help'.
+  $ sudo apt-get update
+  $ sudo apt-get install git-annex
+\end{lstlisting}
+\bigskip
+
 First, we make an empty repository:
 \begin{lstlisting}
   $ mkdir annex_project
@@ -56,18 +80,4 @@ You can now remove the big data file from the original repository.
 \end{lstlisting}
 
 But you can not remove it from the clone.
-
-\subsubsection*{Project skeleton.}
-Search for the ``Project skeleton''.
-\begin{itemize}
-  \item \emph{Hint:} Click the ``Public area'' icon and use the search option.
-\end{itemize}
-\bigskip
-
-Suppose you are going to do an RNASeq analysis. You have the following files:
-\begin{itemize}
-  \item read\_1.fq
-  \item read\_2.fq
-  \item Makefile
-\end{itemize}
 \end{document}