Skip to content
GitLab
Menu
Projects
Groups
Snippets
Help
Help
Support
Community forum
Keyboard shortcuts
?
Submit feedback
Contribute to GitLab
Sign in
Toggle navigation
Menu
Open sidebar
courses
Git course
Commits
756874cc
Commit
756874cc
authored
Jun 22, 2014
by
Laros
Browse files
Updated the skeleton lecture and handouts.
parent
d42938da
Changes
4
Hide whitespace changes
Inline
Side-by-side
skeleton/markdown.html
0 → 100644
View file @
756874cc
<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
<html
xmlns=
"http://www.w3.org/1999/xhtml"
>
<head>
<meta
http-equiv=
"Content-Type"
content=
"text/html; charset=utf-8"
/>
<meta
http-equiv=
"Content-Style-Type"
content=
"text/css"
/>
<meta
name=
"generator"
content=
"pandoc"
/>
<title></title>
<style>
div
.padded
{
padding-left
:
30px
;
padding-right
:
30px
;
}
</style>
<link
href=
"https://git.lumc.nl/assets/application-9e18d69ef3096721155fd862af466f51.css"
media=
"all"
rel=
"stylesheet"
/>
</head>
<body>
<div
class=
"padded"
>
<h1
id=
"installation"
>
Installation
</h1>
<p>
To install
<a
href=
"http://www.git-scm.com/"
>
Git
</a>
:
</p>
<pre><code>
apt-get install git
</code></pre>
<p>
Now you can do the following:
</p>
<ul>
<li>
Make a new repository with
<code>
git init
</code>
.
</li>
<li>
Clone an existing repository with
<code>
git clone
</code>
.
</li>
</ul>
</div>
</body>
</html>
skeleton/markdown.xcf
0 → 100644
View file @
756874cc
File added
skeleton/skeleton.tex
View file @
756874cc
...
...
@@ -54,10 +54,10 @@
\begin{pframe}
Usage:
\begin{itemize}
\item
Make a
\emph
{
fork
}
(copy)
of the skeleton project.
\item
Make a
clone
of the skeleton project.
\item
Rename the project.
\item
C
lone your project
.
\item
Start working with i
t.
\item
C
reate a new project on the server
.
\item
Change the remote
\bt
{
origin
}
to your new projec
t.
\end{itemize}
\bigskip
\pause
...
...
@@ -76,35 +76,6 @@
\permfoot
{
https://git.lumc.nl/lgtc-bioinformatics/project-skeleton
}
\end{pframe}
%\subsection{Forking}
%\begin{pframe}
% 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{pframe}
%\subsection{Configuration}
%\begin{pframe}
% 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{pframe}
\section
{
Project structure
}
\subsection
{
Global overview
}
\begin{pframe}
...
...
@@ -117,10 +88,35 @@
\end{itemize}
\bigskip
Ideally, every directory in the project has a
\bt
{
README
}
file.
Ideally, every directory in the project has a
\bt
{
README.md
}
file.
\end{pframe}
\subsection
{
Markdown files
}
\begin{pframe}
\begin{lstlisting}
[language=none, caption=Markdown snippet.]
# Installation
To install [Git](http://www.git-scm.com/):
apt-get install git
Now you can do the following:
- Make a new repository with `git init`.
- Clone an existing repository with `git clone`.
\end{lstlisting}
\end{pframe}
\begin{pframe}
\begin{figure}
[]
\begin{center}
\includegraphics
[width=\textwidth]
{
markdown
}
\end{center}
\caption
{
Rendered markdown page.
}
\end{figure}
\end{pframe}
\subsection
{
The toplevel ``README'' file
}
\subsection
{
The toplevel ``README
.md
'' file
}
\begin{pframe}
This file contains general information about the project, for example:
\begin{itemize}
...
...
@@ -148,7 +144,7 @@
Used to store all raw data.
\bigskip
The
\bt
{
README
}
contains:
The
\bt
{
README
.md
}
contains:
\begin{itemize}
\item
Description of the delivered data.
\begin{itemize}
...
...
@@ -174,6 +170,7 @@
\begin{pframe}
All analysis related files are stored here:
\begin{itemize}
\item
Symlinks to the actual data.
\item
Run scripts.
\item
Make files.
\item
Result files.
...
...
@@ -181,7 +178,7 @@
\bigskip
Try to separate self-contained parts of the analysis in their own
subdirectories and document dependencies in a
\bt
{
README
}
file.
subdirectories and document dependencies in a
\bt
{
README
.md
}
file.
\begin{itemize}
\item
Normal data analysis.
\item
$
k
$
-mer analysis.
...
...
@@ -263,6 +260,20 @@
\end
{
lstlisting
}
\end
{
pframe
}
\subsection
{
Modifying files
}
\begin
{
pframe
}
Sometimes we need to change the content of a file.
\bigskip
\begin
{
lstlisting
}
[
language
=
none, caption
=
Unlocking a file.
]
$
git annex edit <filename>
unlock <filename> (copying...) ok
\end{lstlisting}
\bigskip
You can use
\bt
{
git annex add
}
when you are done.
\end{pframe}
\subsection
{
Removing files
}
\begin{pframe}
As long as there are enough copies available, you can remove files.
...
...
@@ -304,6 +315,29 @@
\end{lstlisting}
\end{pframe}
\subsection
{
Cleaning your repository
}
\begin{pframe}
You can clean your repository with one command.
\bigskip
\begin{lstlisting}
[language=none, caption=Remove untracked files.]
$
git clean
-
f
-
x
\end
{
lstlisting
}
\begin
{
table
}
[]
\begin
{
center
}
\begin
{
tabular
}{
ll
}
option
&
description
\\
\hline
\bt
{
-
f
}
&
Force
(
really remove
)
.
\\
\bt
{
-
x
}
&
Also remove
\emph
{
ignored
}
files.
\\
\bt
{
-
n
}
&
Do a
\emph
{
dry run
}
.
\\
\end
{
tabular
}
\end
{
center
}
\caption
{
Common options.
}
\end
{
table
}
\end
{
pframe
}
\subsection
{
Working together on the same clone
}
\begin
{
pframe
}
Sometimes you need to work with other people on the same repository clone.
...
...
@@ -331,8 +365,9 @@
Martijn Vermaat
Zuotian Tatum
Wibowo Arindrarto
Zuotian Tatum
\end
{
center
}
\vfill
...
...
skeleton/skeleton_handouts.tex
View file @
756874cc
...
...
@@ -71,6 +71,13 @@ With the ``\texttt{file}'' command you can now see that
$
git pull
$
git annex get bigfile.dat
\end{lstlisting}
\newpage
Let the original repository know that you have a copy.
\begin{lstlisting}
$
git annex sync
\end
{
lstlisting
}
\bigskip
You can now remove the big data file from the original repository.
...
...
Write
Preview
Supports
Markdown
0%
Try again
or
attach a new file
.
Attach a file
Cancel
You are about to add
0
people
to the discussion. Proceed with caution.
Finish editing this message first!
Cancel
Please
register
or
sign in
to comment