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# Preparations for course: Code and data management with Git
- 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)
- Szymon Kiełbasa (S.M.Kielbasa@lumc.nl)
## Program
Very preliminary, please update, extend, or comment.
| Time | Subject | Teacher | Contents |
| ----- | ----------------- | ----------------- | ------------------------- |
| 09:00 | **Introduction** | Jeroen Laros | Welcome, GitLab overview |
| 09:30 | *Practical* | | |
| 09:45 | **Git basics** | Wibowo Arindrarto | Basic Git command line fu |
| 10:15 | *Practical* | | |
| 10:45 | Coffee | | |
| 11:00 | **Git remotes** | Martijn Vermaat | Collaborating via GitLab |
| 11:30 | *Practical* | | |
| 12:00 | Lunch | | |
| 13:00 | **Git conflicts** | Martijn Vermaat? | Merge conflicts, protected branches |
| 13:30 | *Practical* | | |
| 14:00 | Break | | |
| 14:30 | **Data analysis** | Szymon Kiełbasa | Project template, R-Studio, GitLab |
| 15:00 | *Practical* | | |
| 15:30 | Leftover minutes | | TODO: assign to some lecture or practical |
| 16:00 | Questions, drinks | | |
- Branches: not in this course
- Git annex: not in this course
## Participants
Confirmed:
1. Angga Fuady
2. Tooba Tabbassidaloii
3. Soheil Yousefi
4. Rick de Leeuw
5. Sake van Pelt
6. Niels de Water
7. Dirk Ages
8. Arjen Langeveld
9. Thomas Chin-A-Woeng
Confirmed (but only if seats available):
1. Magnus Palmblad
2. Arzu Tugce Guler
3. Jonathan Vis
Cancelled:
1. Johan den Dunnen
2. Martijn Eenink
3. Roel Zinkstok
4. Saeed Katiraei
5. Tarek Malas
## Course materials
We can reuse many slides from last year, see the contents of this repository.
We will provide the course materials and program via GitLab. So this GitLab
project will be the course homepage.
The old course homepage can still be found here, but will be deleted before the
course starts: https://humgenprojects.lumc.nl/trac/humgenprojects/wiki/gitcourse
# 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 the necessary
software installed (see [Software installation](https://humgenprojects.lumc.nl/trac/humgenprojects/wiki/gitcourse/SoftwareInstallation)).
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.
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README.md
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# Code and data management with Git # Code and data management with Git
This is the website for the course *Code and data management with Git*. This This is the website for the course *Code and data management with Git*. This
course consists of a introduction to working with the [Git](http://git-scm.com/) course consists of an introduction to working with the
version control system for data analysis and is aimed primarily at researchers [Git](http://git-scm.com/) version control system for data analysis and is
in the LUMC. aimed primarily at researchers in the LUMC.
The Git system is widely used by software developers, but can also be used for 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 project management. In the LUMC we use [GitLab](https://git.lumc.nl) as a
...@@ -12,11 +12,82 @@ history, etc, GitLab makes your projects more reproducible and collaboration ...@@ -12,11 +12,82 @@ history, etc, GitLab makes your projects more reproducible and collaboration
with colleagues easy. with colleagues easy.
## Course dates ## 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)
- Szymon Kiełbasa (S.M.Kielbasa@lumc.nl)
## 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.
| Time | Subject | Teacher | Contents |
| ----- | ----------------- | ----------------- | ------------------------- |
| 09:00 | **Introduction** | Jeroen Laros | Welcome, GitLab overview, SSH keys |
| 09:30 | *Practical* | | |
| 09:45 | **Git basics** | Wibowo Arindrarto | Basic Git command line fu |
| 10:30 | *Practical* | | |
| 11:00 | Coffee | | |
| 11:15 | **Git remotes** | Martijn Vermaat | Sharing and collaborating via GitLab |
| 11:45 | *Practical* | | |
| 12:00 | Lunch | | |
| 13:00 | *Practical* | | |
| 13:30 | **Git conflicts** | Martijn Vermaat | Resolving merge conflicts, protected branches |
| 14:15 | *Practical* | | |
| 14:45 | Break | | |
| 15:00 | **Data analysis** | Szymon Kiełbasa | More GitLab, Markdown, data analysis use case |
| 15:30 | *Practical* | | |
| 16:00 | Questions, drinks | | |
## 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
[Linux](http://en.wikipedia.org/wiki/Linux), but Git also runs on Mac OSX. On
Windows, it is probably easiest to use something like
[MobaXterm](http://mobaxterm.mobatek.net/) or
[VirtualBox](https://www.virtualbox.org/) with
[Ubuntu](http://www.ubuntu.com/).
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
- (Code School - Try Git)[https://try.github.io/] (you could even try this
before the course)
- (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]
(useful for printing)
## Past course dates
- October 14th, 2013: Git introduction course - October 14th, 2013: Git introduction course
- June 23rd, 2014: Git introduction course - June 23rd, 2014: Git introduction course
- **December 1st, 2015: Code and data management with Git** ([preparations](PREPARATIONS.md)) - December 1st, 2015: Code and data management with Git
For corresponding snapshots of this repository, see [tags](https://git.lumc.nl/humgen/gitcourse/tags). For corresponding snapshots of this repository, see [tags](https://git.lumc.nl/humgen/gitcourse/tags).
...@@ -39,4 +110,4 @@ First clone this repository, then fetch the data from the submodule: ...@@ -39,4 +110,4 @@ First clone this repository, then fetch the data from the submodule:
A new presentation can be added like this: A new presentation can be added like this:
cd presentation cd presentation
bash mkpres.sh ../mypresentation bash mkpres.sh ../mypresentation
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