Starting a new bioinformatics project - The-Bioinformatics-Group/Albiorix GitHub Wiki

[Work in progress]

Why this page

Starting a new bioinformatics project is easy and fun. However, managing the files and sharing the results with your colleges can be challenging and archiving a finished project can be a total nightmare. It's therefore useful to adopt some data management best practices early in once career. This tutorial presents a method for setting up a new bioinformatics project that is well documented, version controlled and well structured using git, github and files with markdown formatted syntax.

For the impatient

  1. Create a git repository on github.com
  2. Clone this repository to the computer where you will run your new bioinformatics project.
  3. Shortly describe the project in the root README.md file
  4. Create a directory for data, code and testing that contains individual README.md files.
  5. Add and edit a .gitignore file in the root directory of the project.
  6. Start working on your project and keep updating your README.md files.

1. Create a repository

Give the repository a short, memorable but still informative name like "Krokodil_SNP_project", "Cactaceae_gene_capture" or "Fucus_genome_project". Check the box next to "Initialize this repository with a README".

Perhaps this could be done using code that created this "boilerplate" stuff? Perhaps automatically commit and push this to github? Perhaps include some template sge scripts in the code directory?