software-development.md

What software development skill do I need?

The first thing is obviously knowing and choosing programming language(s) appropriate for your task. Here's a short discussion on that here: {ref}content:programming_languages

Let's say you are writing a super cool software that does amazing things.

You should version control it using Git.

And you should want to make it open-source and f

Surely, you want the world to use it. If your software has a lot of dependencies, you might want to containerize it.

Version control using Git and GitHub

• https://www.w3schools.com/git/

Conda

• https://conda.io/projects/conda/en/latest/user-guide/getting-started.html

When you install a package via Conda, it searches for the package in repositories (called channels). If the package is not available in Conda's default channel, alternative channels include conda-forge and Bioconda. We recommend using conda-forge for the reasons listed here.

Note that Conda's dependency resolution tends to be slow, so here are some faster alternatives:

• Miniconda: https://docs.anaconda.com/free/miniconda/
• Micromamba: https://mamba.readthedocs.io/en/latest/user_guide/micromamba.html

Docker

• https://docs.docker.com/
• Collection of useful bioinformatics Docker images: https://pegi3s.github.io/dockerfiles/

Apptainer

• https://apptainer.org/docs/user/main/quick_start.html

Documentation

• Sphinx (Python): https://www.sphinx-doc.org/en/master/
• Jupyter Book: https://jupyterbook.org/en/stable/intro.html

GitHub Actions

• https://docs.github.com/en/actions/quickstart