... | ... | @@ -23,43 +23,43 @@ Another advantage is to get help from the bioinformatics team for a code review |
|
|
What it is?
|
|
|
-----------
|
|
|
|
|
|
The idea behind this initiative is to provide one safe, shared and controlled environment where all MIB could make their scripts, tutorials, teaching material, papers... accessible to the other and potentially with external collaborators.
|
|
|
The idea behind this initiative is to provide one safe, shared and controlled environment where all MIB could make their scripts, tutorials, teaching material, papers... accessible MIB-wide and with potential external collaborators.
|
|
|
No data (genomic) will/should be hosted in that environment. It does not replace your "external" personal account but it should be used for all work (WUR) related code.
|
|
|
|
|
|
Who has access to it?
|
|
|
---------------------
|
|
|
|
|
|
The WUR git (https://git.wur.nl) is open to all WUR members by default. If you do not use it yet, we recommend you do so and request access to <MIB repository>. An account can be arranged for external collaborators if needed.
|
|
|
This git space is maintained and administered by MIB Bioinfo. By default the locations reserved for papers and teaching documents are opened world-wide (anyone can see and download them), the space reserved to code is restricted by default but could be made public on request or depending on the license strategy. MIB users can request write access rights by email to bioinfo.mib@wur.nl.
|
|
|
The WUR git (https://git.wur.nl) is open to all WUR members by default. If you do not use it yet, we recommend you do so and request access to [MIB project](https://git.wur.nl/afsg-microbiology). An account can be arranged for external collaborators if needed.
|
|
|
This git space is maintained and administered by MIB Bioinfo. By default the locations reserved for papers and teaching documents are opened world-wide (anyone can see and download them), the space reserved to code is restricted to MIB only by default but could be made public on request. MIB users can request write access rights by email to bioinfo.mib@wur.nl.
|
|
|
|
|
|
|
|
|
Preferably, development should be made in your personal space on gitlab then make a pull request to the correct repository on MIB gitlab. The bioinfo will make sure the code is usable and well described.
|
|
|
|
|
|
Organisation and accessibility
|
|
|
------------------------------
|
|
|
Structure and description of the folders
|
|
|
----------------------------------------
|
|
|
|
|
|
The environment consists of 4 directories, see below for explanations. More directories & sub-directories could be made when needed.
|
|
|
The environment consists of 4 directories at the moment, more directories & sub-directories can be added.
|
|
|
|
|
|
*Documentation:*
|
|
|
**Documentation:**
|
|
|
This repository will be used to share all documentation and template about the MIB git.
|
|
|
Wiki can be found via the following [link](https://git.wur.nl/afsg-microbiology/documentation/-/wikis/home)
|
|
|
templates can be found at [https://git.wur.nl/afsg-microbiology/documentation/-/tree/main](https://git.wur.nl/afsg-microbiology/documentation/-/tree/main)
|
|
|
|
|
|
*Education:*
|
|
|
**Education:**
|
|
|
This folder is meant to host material dedicated to education such as courses presentations or tutorials.
|
|
|
The subject does not matter, in principle molecular biology and hardcore linux tutorials can be part of this folder. Making subfolders can help organising the documents, you can request subfolders via email to bioinfo.mib@wur.nl.
|
|
|
This folder is visible world-wide, MIB members can request write access.
|
|
|
|
|
|
|
|
|
*Scripts:*
|
|
|
**Scripts:**
|
|
|
Any specialised script or utility script will be placed in this repository. Take a look at [templates] folder and good coding practices to get ideas on how to make your code publishable. The development phase is always made in your personal repositories then shared via a "pull request" to this repository or take contact with bioinfo.mib@wur.nl by email.
|
|
|
|
|
|
|
|
|
|
|
|
*Pipelines:*
|
|
|
**Pipelines:**
|
|
|
This part of the space is reserved for more complex scripts that full processing of data. Also use "pull request" to have your pipeline published here.
|
|
|
|
|
|
*Publication Supplementary Material:*
|
|
|
**Publication Supplementary Material:**
|
|
|
Each publications should have a repository here, The abstract can be copied to the README file.
|
|
|
The name of the repository should follow this format, DATE_FirstAuthorName_...
|
|
|
Supplementary materials could be placed in the repository, make sure all "big" files are compressed.
|
... | ... | |