Commit b3427d8d authored by Jeroen F.J. Laros's avatar Jeroen F.J. Laros

Updated the skeleton presentation and handouts.

parent bf182669
......@@ -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}.
......
......@@ -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}
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