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 @@ ...@@ -50,41 +50,19 @@
\end{itemize} \end{itemize}
\end{frame} \end{frame}
\begin{frame} \section{Starting a project}
\begin{fframe}
\frametitle{Project skeleton.} \frametitle{Project skeleton.}
That is why we made a \emph{skeleton} project.
\bigskip
Usage: Usage:
\begin{itemize} \begin{itemize}
\item Make a \emph{fork} (copy) of the skeleton project. \item Make a \emph{fork} (copy) of the skeleton project.
\item Rename the project. \item Rename the project.
\item Do a checkout. \item Clone your project.
\item Start working with it. \item Start working with it.
\end{itemize} \end{itemize}
\end{frame} \bigskip
\pause
\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}
Configure your project. Configure your project.
\begin{itemize} \begin{itemize}
...@@ -95,7 +73,41 @@ ...@@ -95,7 +73,41 @@
\end{itemize} \end{itemize}
\item Add the people that work on this project. \item Add the people that work on this project.
\end{itemize} \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} \section{Project structure}
\begin{frame} \begin{frame}
...@@ -129,7 +141,7 @@ ...@@ -129,7 +141,7 @@
Documentation on the project: Documentation on the project:
\begin{itemize} \begin{itemize}
\item Annotated sample lists. \item Annotation of the data.
\item Goal of the project. \item Goal of the project.
\item Related work and literature. \item Related work and literature.
\begin{itemize} \begin{itemize}
...@@ -206,6 +218,14 @@ ...@@ -206,6 +218,14 @@
\end{itemize} \end{itemize}
\bigskip \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 We do want to have some way to track our input and output data. This can be
done with \bt{git-annex}. done with \bt{git-annex}.
......
...@@ -14,7 +14,31 @@ Project skeleton practical. ...@@ -14,7 +14,31 @@ Project skeleton practical.
\end{center} \end{center}
\bigskip \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.} \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: First, we make an empty repository:
\begin{lstlisting} \begin{lstlisting}
$ mkdir annex_project $ mkdir annex_project
...@@ -56,18 +80,4 @@ You can now remove the big data file from the original repository. ...@@ -56,18 +80,4 @@ You can now remove the big data file from the original repository.
\end{lstlisting} \end{lstlisting}
But you can not remove it from the clone. 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} \end{document}
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