skeleton_handouts.tex 1.65 KB
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\documentclass{article}
\usepackage{fullpage}
\usepackage{listings}

\frenchspacing
\setlength{\parindent}{0pt}
\pagestyle{empty}

\begin{document}
\begin{center}
{\bf Git Introduction Course}

Project skeleton practical.
\end{center}
\bigskip

\subsubsection*{Git annex.}
First, we make an empty repository:
\begin{lstlisting}
  $ mkdir annex_project
  $ cd annex_project
  $ git init
  $ git annex init "Original repository."
\end{lstlisting}
\bigskip

Now add a ``big file'' and annex it.
\begin{lstlisting}
  $ dd if=/dev/urandom of=bigfile.dat count=1024
  $ git annex add bigfile.dat
  $ git commit -m "Added big file."
\end{lstlisting}
\bigskip

Now, we clone the project and let this repository know where the clone is.
\begin{lstlisting}
  $ git clone . ../annex_clone
  $ git remote add annex_clone ../annex_clone
  $ cd ../annex_clone
  $ git annex init "Cloned repository."
\end{lstlisting}
\bigskip

With the ``\texttt{file}'' command you can now see that
``\texttt{bigdata.dat}'' is not present in this repository.
\begin{lstlisting}
  $ git pull
  $ git annex get bigfile.dat
\end{lstlisting}
\bigskip

You can now remove the big data file from the original repository.
\begin{lstlisting}
  $ cd ../annex_project
  $ git annex drop bigfile.dat
\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}