Commit a8853c06 authored by Szymon M. Kiełbasa's avatar Szymon M. Kiełbasa

usecases

parent d961384b
......@@ -27,7 +27,7 @@ Very preliminary, please update, extend, or comment.
| 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 |
| 14:30 | **Data analysis** | Szymon Kiełbasa | [GitLab use cases: markdown, reproducible reports from Rstudio](usecases/) |
| 15:00 | *Practical* | | |
| 15:30 | Leftover minutes | | TODO: assign to some lecture or practical |
| 16:00 | Questions, drinks | | |
......@@ -85,4 +85,4 @@ is more than enough, or you could go though [tutorials 1-3 here](http://www.ee.s
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.
\ No newline at end of file
installed. The lessons are interactive, meaning that you really need a laptop.
......@@ -9,7 +9,7 @@ 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
with colleagues easy.
with colleagues easy ([introduction](http://doc.gitlab.com/ce/gitlab-basics/README.html)).
## Course dates
......@@ -39,4 +39,4 @@ First clone this repository, then fetch the data from the submodule:
A new presentation can be added like this:
cd presentation
bash mkpres.sh ../mypresentation
\ No newline at end of file
bash mkpres.sh ../mypresentation
# [gitlab](https://www.gitlab.com) and `git` use cases live demo
- [markdown](https://github.com/adam-p/markdown-here/wiki/Markdown-Cheatsheet) language
- `README.md` file
- editing in the browser
- use case: meeting minutes
- project location and access permisions:
- access levels
- groups and individuals
- use case: bioinformatics analysis:
- project skeletons
- integration with [Rstudio](https://www.rstudio.com/):
- example report in R/[Rmarkdown](http://rmarkdown.rstudio.com/)
- interaction with collaborators:
- delivering reports through [gitlab](https://www.gitlab.com)
- checking updates (commit logs and graphs)
- [tagging](https://git-scm.com/book/en/v2/Git-Basics-Tagging) repository states
- requesting changes ([issues](http://doc.gitlab.com/ce/gitlab-basics/create-issue.html))
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