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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 (preliminary!)
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- Date: April 25th, 2016
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- Time: 9:00 - 17:00
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- Location: 02-T-00-008
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- 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 (preliminary!)
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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 |
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| 10:30 | [Practical](/uploads/5590b3f6eb6976d92b4d153b906543b3/basics_handouts.pdf)             |                   |                           |
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| 11:00 | Coffee                                                                                 |                   |                           |
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| 11:15 | [Git and remote repositories](/uploads/fae0409963d991c25221843288ed3368/remotes.pdf)   | Martijn Vermaat   | Sharing and collaborating via GitLab |
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| 12:00 | Lunch                                                                                  |                   |                           |
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| 13:00 | [Practical](/uploads/bd5d6574d2534d3a7afaf3d43bf70aaf/remotes_handouts.pdf)            |                   |                           |
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| 13:30 | [Combining changes by merging](/uploads/af01008ba3e6f2c0e1742dc292690e22/merging.pdf)  | Martijn Vermaat   | Commit graph, merging, resolving merge conflicts |
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| 14:15 | [Practical](/uploads/b9649d50b3146eaf4632efc80f143f54/merging_handouts.pdf)            |                   |                           |
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| 14:45 | Break                                                                                  |                   |                           |
| 15:00 | [Data analysis](usecases/)                                                             | Szymon Kiełbasa   | More GitLab, Markdown, data analysis use case |
| 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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- April 25th, 2016: 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