README.md 5.4 KB
Newer Older
Martijn Vermaat's avatar
Martijn Vermaat committed
1
# Code and data management with Git
Laros's avatar
Laros committed
2

Martijn Vermaat's avatar
Martijn Vermaat committed
3
This is the website for the course *Code and data management with Git*. This
Vermaat's avatar
Vermaat committed
4 5 6
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.
Vermaat's avatar
Vermaat committed
7

Martijn Vermaat's avatar
Martijn Vermaat committed
8 9 10 11
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
Vermaat's avatar
Vermaat committed
12
with colleagues easy ([introduction](http://doc.gitlab.com/ce/gitlab-basics/README.html)).
Vermaat's avatar
Vermaat committed
13 14


Vermaat's avatar
Vermaat committed
15 16 17 18 19 20 21 22 23
## 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)
Kielbasa's avatar
Kielbasa committed
24
  - Szymon M. Kiełbasa (S.M.Kielbasa@lumc.nl)
Vermaat's avatar
Vermaat committed
25 26 27 28 29 30 31 32


## 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.

33 34 35 36 37
| 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 |
Vermaat's avatar
Vermaat committed
38
| 10:30 | [Practical](/uploads/5590b3f6eb6976d92b4d153b906543b3/basics_handouts.pdf)             |                   |                           |
39
| 11:00 | Coffee                                                                                 |                   |                           |
Vermaat's avatar
Vermaat committed
40
| 11:15 | [Git and remote repositories](/uploads/fae0409963d991c25221843288ed3368/remotes.pdf)   | Martijn Vermaat   | Sharing and collaborating via GitLab |
41
| 12:00 | Lunch                                                                                  |                   |                           |
Vermaat's avatar
Vermaat committed
42 43 44
| 13:00 | [Practical](/uploads/bd5d6574d2534d3a7afaf3d43bf70aaf/remotes_handouts.pdf)            |                   |                           |
| 13:30 | [Combining changes by merging](/uploads/89a6d236332f607b1c091448836efc87/merging.pdf)  | Martijn Vermaat   | Commit graph, merging, resolving merge conflicts |
| 14:15 | [Practical](/uploads/b9649d50b3146eaf4632efc80f143f54/merging_handouts.pdf)            |                   |                           |
45 46 47
| 14:45 | Break                                                                                  |                   |                           |
| 15:00 | [Data analysis](usecases/)                                                             | Szymon Kiełbasa   | More GitLab, Markdown, data analysis use case |
| 16:00 | Questions, drinks                                                                      |                   |                           |
Vermaat's avatar
Vermaat committed
48 49 50 51 52 53 54 55 56 57 58 59


## 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
Martijn Vermaat's avatar
Martijn Vermaat committed
60 61
[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).
Vermaat's avatar
Vermaat committed
62 63 64 65 66 67 68 69

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

Vermaat's avatar
Vermaat committed
70
- [Code School - Try Git](https://try.github.io/) (you could even try this
Vermaat's avatar
Vermaat committed
71
  before the course)
Vermaat's avatar
Vermaat committed
72 73 74 75 76 77
- [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)
Vermaat's avatar
Vermaat committed
78 79 80 81
  (useful for printing)


## Past course dates
Vermaat's avatar
Vermaat committed
82

Martijn Vermaat's avatar
Martijn Vermaat committed
83 84
- October 14th, 2013: Git introduction course
- June 23rd, 2014: Git introduction course
Vermaat's avatar
Vermaat committed
85
- December 1st, 2015: Code and data management with Git
Vermaat's avatar
Vermaat committed
86

Martijn Vermaat's avatar
Martijn Vermaat committed
87
For corresponding snapshots of this repository, see [tags](https://git.lumc.nl/humgen/gitcourse/tags).
Vermaat's avatar
Vermaat committed
88 89


Martijn Vermaat's avatar
Martijn Vermaat committed
90
## Using the course materials
Vermaat's avatar
Vermaat committed
91

Martijn Vermaat's avatar
Martijn Vermaat committed
92 93 94 95 96 97 98 99 100 101
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
Vermaat's avatar
Vermaat committed
102 103 104 105 106 107
    git submodule init
    git submodule update

A new presentation can be added like this:

    cd presentation
Vermaat's avatar
Vermaat committed
108
    bash mkpres.sh ../mypresentation