Commit 711bf673 authored by Laurent Heirendt's avatar Laurent Heirendt

Merge branch 'develop' into 'master'

Regular merge of develop

See merge request !122
parents 590e3771 98b253a7
Pipeline #23642 passed with stage
in 47 seconds
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---
# Git clients
## Installation of Git
You can find installers for Windows, MacOS and Linux on the [Git webpage](https://git-scm.com/downloads).
Installation instructions are provided [here](https://howto.lcsb.uni.lu/?contribute:install-git).
## GUI clients
......@@ -30,4 +28,4 @@ There are also several IDEs (integrated development environments) that have git
* [Visual Studio Code](https://code.visualstudio.com/)
* [Atom](https://atom.io/)
* [IntelliJ](https://www.jetbrains.com/idea/)
* [PyCharm](https://www.jetbrains.com/pycharm/)
* [PyCharm](https://www.jetbrains.com/pycharm/)
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layout: page
permalink: /external/contribute/install-git/
shortcut: contribute:install-git
redirect_from:
- /cards/contribute:install-git
- /external/cards/contribute:install-git
---
# Installation of Git
Several git clients are presented [here](https://howto.lcsb.uni.lu/?contribute:git-clients).
For most of the git clients, `git` is actually required to be installed on the system. You can find installers for Windows, MacOS and Linux on the [Git webpage](https://git-scm.com/downloads).
If you are using Visual Studio Code, and if you want to contribute to a repository hosted on the [LCSB Gitlab](https://git-r3lab.uni.lu), you will need to verify the host key first before you are able to clone or push to a repository. For this, open a terminal (on Linux or macOS) or Git Bash (on Windows), and type:
```bash
ssh git@git-r3lab-server.uni.lu -p8022
```
Then, press Enter and type `yes`. This will add the git-r3lab server to the known hosts on your system.
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layout: page
permalink: /external/integrity/organization/
shortcut: integrity:organization
redirect_from:
- /cards/integrity:organization
- /external/cards/integrity:organization
---
# Organization
## Process of organizing files and folders
The present suggestions are to guide individual researchers and staff members. It is important to note that certain research groups already have specific group guidelines in place.
## Structure of folders
Organizing files in directories is a key task to stay organized and to make sure that everyone is
able to find back the files easily.
A key rule is to name the folders with straightforward but explicit names, and to include the decision tree of where to put a given file inside the folder structure. In fact, the directory tree should in some sense
reflect the decision tree.
More details on naming files and folders are provided in the dedicated [file naming card](https://howto.lcsb.uni.lu/?integrity:naming).
## Suggestions
There are a few suggestions to organize a folder structure:
### Suggestion 1
Only have a few folders per level (i.e. 5-6 folders per level). That way, the decision of where to include a file is straightforward.
### Suggestion 2
The more general the upper levels and the more precise the lower levels are, the easier it is for someone to decide where to include a respective file. The idea is to mirror a real tree.
### Suggestion 3
Depending on the setup of the research group, it might be useful to structure the group's overall mission into separate programs, sub-missions, or areas of expertise.
### Suggestion 4
Archived folders (or frozen folders) can be named with an `_` (underscore) preceding the actual name of the folder.
## Example
An example for a folder of research group at LCSB:
```
LCSB_GRPNAME
├── _alumni
│ ├── firstLast1
│ └── firstLast2
├── grants
│ ├── grant1
│ └── grant2
├── programs
│ ├── program1
│ │ ├── _project0
│ │ ├── project1
│ │ │ ├── papers
│ │ │ │ ├── paper1
│ │ │ │ │ ├── analysis
│ │ │ │ │ ├── figures
│ │ │ │ │ ├── manuscript
│ │ │ │ │ └── rawData
│ │ │ │ └── paper2
│ │ │ │ ├── analysis
│ │ │ │ ├── figures
│ │ │ │ ├── manuscript
│ │ │ │ └── rawData
│ │ │ ├── posters
│ │ │ └── presentations
│ │ └── project2
│ └── program2
├── resources
│ ├── courses
│ ├── hardware
│ ├── literature
│ ├── personnel
│ └── software
├── students
│ ├── firstLast1
│ └── firstLast2
└── team
├── achievements
└── meetingNotes
```
## Specific guidelines for raw data
In the `rawData` folder, of each paper, you should include
* Links to data
* Links to lab books (Paper)
* PDF of book if ELN
When using data collection platforms, make sure that you follow their specific guidelines. Avoid the use of personal folders for raw data storage.
Generally, the following is often the case depending on the type of data:
* **Common data**: Export raw data where possible and store it on one of the storage locations defined above or as defined in the group guidelines.
* **Group specific data**: Export raw data where possible and store it on one of the storage locations defined above or as defined in the group guidelines. Make sure all raw data is properly backed up.
* **Platform specific data**: Export or retrieve raw data where possible and store it on one of the storage locations defined defined above, as defined in the group guidelines, or as defined in the platform-specific guidelines. No backups will be provided by the platform.
## Specific guidelines for ELN
In general, make sure that all lab books (paper and electronic versions) exist and are available to somebody from the group. By default, all ELN should be readable by the group.
......@@ -29,6 +29,7 @@ The How-to cards are intended to provide practical guidance in implementing Data
<ul>
<li><a href="external/contribute/add-edit-card">How to add or edit a howto card</a></li>
<li><a href="external/contribute/git-clients">Git clients</a></li>
<li><a href="external/contribute/install-git">Installation of Git</a></li>
<li><a href="external/contribute/markdown">Markdown</a></li>
</ul>
......@@ -57,7 +58,8 @@ The How-to cards are intended to provide practical guidance in implementing Data
<li><a href="external/integrity/encryption/disk">Encrypting the Startup Disk for Your Laptop/Desktop</a></li>
<li><a href="external/integrity/encryption/file">Encrypting Files and Folders</a></li>
<li><a href="external/integrity/naming">Naming files</a></li>
<li><a href="external/integrity/organization">Organization</a></li>
</ul>
</div>
</div>
</div>
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