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

usecases

parent d961384b
...@@ -27,7 +27,7 @@ Very preliminary, please update, extend, or comment. ...@@ -27,7 +27,7 @@ Very preliminary, please update, extend, or comment.
| 13:00 | **Git conflicts** | Martijn Vermaat? | Merge conflicts, protected branches | | 13:00 | **Git conflicts** | Martijn Vermaat? | Merge conflicts, protected branches |
| 13:30 | *Practical* | | | | 13:30 | *Practical* | | |
| 14:00 | Break | | | | 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* | | | | 15:00 | *Practical* | | |
| 15:30 | Leftover minutes | | TODO: assign to some lecture or practical | | 15:30 | Leftover minutes | | TODO: assign to some lecture or practical |
| 16:00 | Questions, drinks | | | | 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 ...@@ -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 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)). 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 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. installed. The lessons are interactive, meaning that you really need a laptop.
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...@@ -9,7 +9,7 @@ The Git system is widely used by software developers, but can also be used for ...@@ -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 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, collaborative environment on top of Git. By keeping track of all versions,
history, etc, GitLab makes your projects more reproducible and collaboration 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 ## Course dates
...@@ -39,4 +39,4 @@ First clone this repository, then fetch the data from the submodule: ...@@ -39,4 +39,4 @@ 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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# [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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