Commit d42938da authored by Jeroen F.J. Laros's avatar Jeroen F.J. Laros

Switched to new template.

parent db9dd5f0
......@@ -2,7 +2,7 @@
\title{Analysis projects skeleton}
\providecommand{\myConference}{Git course}
\providecommand{\myDate}{Monday, October 14, 2013}
\providecommand{\myDate}{Monday, June 23, 2014}
\author{Jeroen F. J. Laros}
\providecommand{\myGroup}{Leiden Genome Technology Center}
\providecommand{\myDepartment}{Department of Human Genetics}
......@@ -31,9 +31,8 @@
% First page of the presentation.
\section{Introduction}
\begin{frame}
\frametitle{Shared projects.}
\subsection{Shared projects}
\begin{pframe}
Most of us work on multiple projects with multiple people.
\bigskip
......@@ -48,12 +47,11 @@
\pause
\item Have the same structure for all projects.
\end{itemize}
\end{frame}
\end{pframe}
\section{Starting a project}
\begin{fframe}
\frametitle{Project skeleton.}
\subsection{Project skeleton}
\begin{pframe}
Usage:
\begin{itemize}
\item Make a \emph{fork} (copy) of the skeleton project.
......@@ -76,11 +74,10 @@
\vfill
\permfoot{https://git.lumc.nl/lgtc-bioinformatics/project-skeleton}
\end{fframe}
\end{pframe}
%\begin{fframe}
% \frametitle{Forking}
%
%\subsection{Forking}
%\begin{pframe}
% Make a new analysis project.
% \begin{itemize}
% \item Go to the ``Project skeleton'' project page on our GitLab server.
......@@ -93,11 +90,10 @@
%
% \vfill
% \permfoot{https://git.lumc.nl/lgtc-bioinformatics/project-skeleton}
%\end{fframe}
%\end{pframe}
%\begin{frame}
% \frametitle{Configuration}
%
%\subsection{Configuration}
%\begin{pframe}
% Configure your project.
% \begin{itemize}
% \item Choose to make your project public or not.
......@@ -107,12 +103,11 @@
% \end{itemize}
% \item Add the people that work on this project.
% \end{itemize}
%\end{frame}
%\end{pframe}
\section{Project structure}
\begin{frame}
\frametitle{Global overview.}
\subsection{Global overview}
\begin{pframe}
Project layout:
\begin{itemize}
\item analysis
......@@ -123,22 +118,20 @@
\bigskip
Ideally, every directory in the project has a \bt{README} file.
\end{frame}
\begin{frame}
\frametitle{The toplevel \bt{\,README\,\,} file.}
\end{pframe}
\subsection{The toplevel ``README'' file}
\begin{pframe}
This file contains general information about the project, for example:
\begin{itemize}
\item Who leads the project.
\item Who participates in the project.
\item The amount of hours people have spent on this project.
\end{itemize}
\end{frame}
\begin{frame}
\frametitle{The \bt{\,doc\,\,} directory.}
\end{pframe}
\subsection{The ``doc'' directory}
\begin{pframe}
Documentation on the project:
\begin{itemize}
\item Annotation of the data.
......@@ -148,11 +141,10 @@
\item You may want to note who provided the documentation.
\end{itemize}
\end{itemize}
\end{frame}
\begin{frame}
\frametitle{The \bt{\,data\,\,} directory.}
\end{pframe}
\subsection{The ``data'' directory}
\begin{pframe}
Used to store all raw data.
\bigskip
......@@ -176,11 +168,10 @@
\end{itemize}
\end{itemize}
\end{frame}
\begin{frame}
\frametitle{The \bt{\,analysis\,\,} directory.}
\end{pframe}
\subsection{The ``analysis'' directory}
\begin{pframe}
All analysis related files are stored here:
\begin{itemize}
\item Run scripts.
......@@ -195,22 +186,20 @@
\item Normal data analysis.
\item $k$-mer analysis.
\end{itemize}
\end{frame}
\begin{frame}
\frametitle{The \bt{\,src\,\,} directory.}
\end{pframe}
\subsection{The ``src'' directory}
\begin{pframe}
Any custom scripts and specific software versions for this project.
\bigskip
When these scripts are useful for other projects, move them to their own
repository.
\end{frame}
\end{pframe}
\section{Working with large files}
\begin{fframe}
\frametitle{Git is not designed for massive files.}
\subsection{Git is not designed for massive files}
\begin{pframe}
Some problems with large files:
\begin{itemize}
\item Limited storage on the server.
......@@ -231,11 +220,10 @@
\vfill
\permfoot{http://git-annex.branchable.com/}
\end{fframe}
\begin{frame}[fragile]
\frametitle{Git annex.}
\end{pframe}
\subsection{Git annex}
\begin{pframe}
Manage files with git, without checking their contents in.
\begin{itemize}
\item Manage large files without storing them.
......@@ -251,11 +239,10 @@
\begin{lstlisting}[language=none, caption=Enable git-annex.]
$ git annex init "<name>"
\end{lstlisting}
\end{frame}
\begin{frame}[fragile]
\frametitle{Adding big files.}
\end{pframe}
\subsection{Adding big files}
\begin{pframe}
In our master repository, we annex a file.
\bigskip
......@@ -274,11 +261,10 @@
<filename>: broken symbolic link to ...
$ git annex get <filename>
\end{lstlisting}
\end{frame}
\begin{frame}[fragile]
\frametitle{Removing files.}
\end{pframe}
\subsection{Removing files}
\begin{pframe}
As long as there are enough copies available, you can remove files.
\bigskip
......@@ -297,11 +283,10 @@
$ rm -rf <repository>
rm: cannot remove <repository>/.git/annex/objects/...
\end{lstlisting}
\end{frame}
\begin{frame}[fragile]
\frametitle{Synchronise your results.}
\end{pframe}
\subsection{Synchronise your results}
\begin{pframe}
Let the other repositories know what you have done.
\bigskip
......@@ -317,11 +302,10 @@
\begin{lstlisting}[language=none, caption=Synchronise with a selection.]
$ git annex sync origin
\end{lstlisting}
\end{frame}
\begin{frame}[fragile]
\frametitle{Working together on the same clone.}
\end{pframe}
\subsection{Working together on the same clone}
\begin{pframe}
Sometimes you need to work with other people on the same repository clone.
\begin{itemize}
\item Where the large files are stored.
......@@ -335,11 +319,11 @@
$ find -type d -exec chmod 775 {} \;
$ find -type f -exec chmod 664 {} \;
\end{lstlisting}
\end{frame}
\end{pframe}
\section{Questions?}
\lastpagetemplate
\begin{fframe}
\begin{pframe}
\begin{center}
Acknowledgements:
\bigskip
......@@ -353,7 +337,7 @@
\vfill
\permfoot{http://git-annex.branchable.com/}
\permfoot{https://git.lumc.nl/lgtc-bioinformatics/project-skeleton}
\end{fframe}
\permfoot{https://git.lumc.nl/lgtc-bioinformatics/project-skeleton}
\end{pframe}
\end{document}
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