Commit 90e92b8e authored by Martijn Vermaat's avatar Martijn Vermaat

Remove old Trac website and program

parent e89090b6
../presentation/Makefile
\ No newline at end of file
\documentclass{article}
\usepackage{fullpage}
\providecommand{\personOne}{Jeroen Laros}
\providecommand{\personTwo}{Martijn Vermaat}
\providecommand{\personThree}{Wibowo Arindrarto}
\providecommand{\myDate}{June 23, 2014}
\providecommand{\myLocation}{Room J1-83, LUMC, Leiden}
\frenchspacing
\setlength{\parindent}{0pt}
\pagestyle{empty}
\begin{document}
\begin{center}
LUMC: Human and Clinical Genetics
{\bf Git Introduction Course}
\myDate
Location: \myLocation
\bigskip
Given by: \personTwo, \personThree\ and \personOne.
\end{center}
\bigskip
This course aims at everyone who works in the Bioinformatics field. We cover a
\emph{version control system} named \texttt{git}. This system is widely used by
software developers, but can also be used for project management. By keeping
track of all versions, history, etc. collaboration with colleagues is easy and
your analysis will be reproducible.
\bigskip
\bigskip
{\bf Program:}
\bigskip
\begin{tabular}{l@{\ -\ }rll}
08:30 & 09:00 & Coffee and registration\\
09:00 & 09:15 & Introduction & \personOne\\
09:15 & 09:30 & Practical 1\\
09:30 & 10:00 & \texttt{git} Basics & \personThree\\
10:00 & 10:30 & Practical 2\\
10:30 & 10:45 & Coffee\\
10:45 & 11:30 & Branching & \personTwo\\
11:30 & 12:00 & Practical 3\\
12:00 & 13:00 & Lunch\\
13:00 & 13:30 & Remotes & \personTwo\\
13:30 & 14:00 & Practical 4\\
14:00 & 14:15 & Break\\
14:15 & 14:45 & Project skeleton / \texttt{git annex} & \personOne\\
14:45 & 15:15 & Practical 5\\
15:15 & 15:45 & Tips and tricks & \personThree\\
15:45 & 16:15 & Practical 6\\
\end{tabular}
\end{document}
#!/bin/sh
src="introduction basics branching remotes skeleton program"
for i in $src; do
cd ../$i
make
mv *.pdf ../website/
make distclean
done
cd ../website
tracwiki commit git
tracwiki attach git *.pdf data.tgz
tracwiki commit git__SLASH__SoftwareInstallation
= Version control with Git course =
This course aims at everyone who works in the Bioinformatics field. We cover a
''version control system'' named ''Git''. This system is widely used by
software developers, but can also be used for project management. By keeping
track of all versions, history, etc. collaboration with colleagues is easy and
your analysis will be reproducible.
The next installment will be on '''June 23'''. Registration is required and handled by MGC. [http://www.medgencentre.nl/ Register at their website].
The June 23, 2014 program can be found [raw-attachment:program.pdf here].
== Prerequisites ==
Affinity with the UNIX shell is required before taking the course. For example, our [wiki:scripting scripting course] is more than enough, or you could go though [http://www.ee.surrey.ac.uk/Teaching/Unix/ tutorials 1-3 here].
We can provide you with a laptop that has all the required software installed. You can also use your own laptop, but make sure it has the necessary software installed (see [wiki:git/SoftwareInstallation Software installation]). The lessons are interactive, meaning that you really need a laptop.
== Course material ==
'''Note: most of this is not yet updated from last year's course.'''
Introduction [raw-attachment:introduction.pdf presentation],
[raw-attachment:introduction_handouts.pdf practical]. [[br]]
Git Basics [raw-attachment:basics.pdf presentation],
[raw-attachment:basics_handouts.pdf practical]. [[br]]
Branching [raw-attachment:branching.pdf presentation],
[raw-attachment:branching_handouts.pdf practical]. [[br]]
Remotes [raw-attachment:remotes.pdf presentation],
[raw-attachment:remotes_handouts.pdf practical]. [[br]]
Project skeleton / `git-annex`
[raw-attachment:skeleton.pdf presentation],
[raw-attachment:skeleton_handouts.pdf practical],
[raw-attachment:data.tgz data]. [[br]]
Git Tips and Tricks [raw-attachment:tips.pdf presentation].
[https://git.lumc.nl/humgen/gitcourse Material sources].
== Further reading ==
- [https://try.github.io/ Code School - Try Git] (you could even try this before the course)
- [http://git-scm.com/book The entire Pro Git book] on the official [http://git-scm.com/ Git website]
- [http://rypress.com/tutorials/git/index.html Ry's Git Tutorial]
- [https://www.atlassian.com/git/tutorial Git tutorials at Atlassian]
- [http://pcottle.github.io/learnGitBranching/ Learn Git Branching]
- [https://git.wiki.kernel.org/index.php/GitCheatSheet Git cheat sheet] (useful for printing)
== Contact ==
Please contact [mailto:m.vermaat.hg@lumc.nl Martijn Vermaat] if you have any questions or comments.
\ No newline at end of file
= Software installation =
We assume you have a system with all software listed below installed '''before''' the course starts.
If you're in the Human Genetics department, Michel can help you by installing all this on your LUMC computer. Simply mention ''git course''.
We work with [http://en.wikipedia.org/wiki/Linux Linux], more specifically Ubuntu (12.04 Quantal Quetzal or later) or Debian Linux (7/Wheezy or later). Git also runs on Windows and Mac OSX, so if you manage to install it on there that's also fine (but note that during the course we will assume Linux).
You can [http://www.ubuntu.com/ download Ubuntu here] and either install it directly on your laptop, or run it inside [https://www.virtualbox.org/ VirtualBox].
We need some system packages to be installed. For the following command, you need sudo rights:
{{{
sudo apt-get install -y git gitg git-annex
}}}
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