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# Code and data management with Git
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This is the website for the course *Code and data management with Git*. This
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course consists of an introduction to working with the
[Git](http://git-scm.com/) version control system for data analysis and is
aimed primarily at researchers in the LUMC.
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The Git system is widely used by software developers, but can also be used for
project management. In the LUMC we use [GitLab](https://git.lumc.nl) as a
collaborative environment on top of Git. By keeping track of all versions,
history, etc, GitLab makes your projects more reproducible and collaboration
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with colleagues easy ([introduction](http://doc.gitlab.com/ce/gitlab-basics/README.html)).
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## Coordinates

- Date: December 1st, 2015
- Time: 9:00 - 17:00
- Location: T-0-010
- Teachers:
  - Martijn Vermaat (m.vermaat.hg@lumc.nl)
  - Jeroen Laros (j.f.j.laros@lumc.nl)
  - Wibowo Arindrarto (W.Arindrarto@lumc.nl)
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  - Szymon M. Kiełbasa (S.M.Kielbasa@lumc.nl)
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## Program

This year the contents will be slightly less advanced on the technical side
(no branching, no git-annex). Instead, there is more focus on using the LUMC
GitLab server and using Git for data analysis projects.

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| Time  | Subject                                                                                | Teacher           | Contents                  |
| ----- | -----------------                                                                      | ----------------- | ------------------------- |
| 09:00 | [Introduction](/uploads/c16e25cadec825ca79a768825f5e64a2/introduction.pdf)             | Jeroen Laros      | Welcome, GitLab overview, SSH keys |
| 09:30 | [Practical](/uploads/59500f585b0b5f06ce4464375f2104a9/introduction_handouts.pdf)       |                   |                           |
| 09:45 | [Git basics](http://bit.ly/lumc_git_basics)                                            | Wibowo Arindrarto | Basic Git command line fu |
| 10:30 | *Practical*                                                                            |                   |                           |
| 11:00 | Coffee                                                                                 |                   |                           |
| 11:15 | **Git and remote repositories**                                                        | Martijn Vermaat   | Sharing and collaborating via GitLab |
| 11:45 | *Practical*                                                                            |                   |                           |
| 12:00 | Lunch                                                                                  |                   |                           |
| 13:00 | *Practical*                                                                            |                   |                           |
| 13:30 | **Combining changes by merging**                                                       | Martijn Vermaat   | Resolving merge conflicts, protected branches |
| 14:15 | *Practical*                                                                            |                   |                           |
| 14:45 | Break                                                                                  |                   |                           |
| 15:00 | [Data analysis](usecases/)                                                             | Szymon Kiełbasa   | More GitLab, Markdown, data analysis use case |
| 15:30 | *Practical*                                                                            |                   |                           |
| 16:00 | Questions, drinks                                                                      |                   |                           |
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## Prerequisites

Affinity with the UNIX shell is required before taking the course. For
example, our
[scripting course](https://humgenprojects.lumc.nl/trac/humgenprojects/wiki/scripting)
is more than enough, or you could go though
[tutorials 1-3 here](http://www.ee.surrey.ac.uk/Teaching/Unix/).

We encourage you to bring your own laptop, but make sure it has a terminal and
[Git](http://git-scm.com/) installed. We work with
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[Linux](http://en.wikipedia.org/wiki/Linux), but Git also runs on Mac OSX.
Windows is not ideal, but here are [some suggestions](WINDOWS.md).
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We can also provide you with a laptop that has all the required software
installed. The lessons are interactive, meaning that you really need a
laptop.


## Further reading

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- [Code School - Try Git](https://try.github.io/) (you could even try this
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  before the course)
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- [The entire Pro Git book](http://git-scm.com/book) on the official [Git
  website](http://git-scm.com/)
- [Ry's Git Tutorial](http://rypress.com/tutorials/git/index.html)
- [Git tutorials at Atlassian](https://www.atlassian.com/git/tutorial)
- [Learn Git Branching](http://pcottle.github.io/learnGitBranching/)
- [Git cheat sheet](https://git.wiki.kernel.org/index.php/GitCheatSheet)
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  (useful for printing)


## Past course dates
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- October 14th, 2013: Git introduction course
- June 23rd, 2014: Git introduction course
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- December 1st, 2015: Code and data management with Git
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For corresponding snapshots of this repository, see [tags](https://git.lumc.nl/humgen/gitcourse/tags).
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## Using the course materials
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There is one [Git submodule](https://git-scm.com/book/en/v2/Git-Tools-Submodules)
on which this repository depends:

- **[presentation](https://git.lumc.nl/j.f.j.laros/presentation)** template for
  presentations in LaTeX.

First clone this repository, then fetch the data from the submodule:

    git clone https://git.lumc.nl/humgen/gitcourse.git
    cd gitcourse
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    git submodule init
    git submodule update

A new presentation can be added like this:

    cd presentation
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    bash mkpres.sh ../mypresentation