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Requirements

You must be on a Unix-based OS (tested with Ubuntu), and have flox and git installed.

For Windows users: it is recommended to use the Windows Subsystem for Linux, AKA: WSL.

For Mac users: If you have a Mac with an Intel processor, this should work as is, but is untested.

warning

Running on Mac is untested and does not include Apptainer because it is unavailable for Darwin with flox.

If you are familiar with conda, flox is a similar tool. In short, flox is like conda for Linux environments, supporting more than just Python, R, and traditional scientific utilities.

You should not need to install conda. Flox allows for custom environment configuration through bash scripting. The flox environments that require conda will install it on the first activation.

Start the Environment​

  1. Clone the Repository with git
# clone
git clone https://github.com/tshanebuckley/ngs_intro.git
# enter the directory
cd ngs_intro
  1. Start the Environment
flox activate

That's pretty much it, you clone the repo and get going!

Repository Structure​

Under the .flox folder, you will find the basic flox environment. As you use this environment and after the initial activation, you will notice that the .flox/lib directory will include a directory with the same name as your user profile. This folder is created and used as your $HOME directory to keep this completely isolated from your main system. This makes cleaning this up as simple as deleting the cloned repository and helps avoid overriding or overlapping with your system.

Everything else are examples to try running yourself. Have fun!

Helper Scripts​

  • Exporting the conda spec file:
# file placed in the ngs_intro directory
export_conda_spec
  • Exporting the conda env yaml file:
# file placed in the ngs_intro directory
export_conda_env
  • Exporting the conda spec file and env yaml file:
# files placed in the ngs_intro directory
export_conda
  • Deleting the completed chapters (so that someone may attempt them from scratch):
# TODO
note

These helper scripts are aliases found in the profile section of the .flox/lib/env/manifest.toml file.