Setting up

Modelblocks relies on a core set of tools to ensure modules can be run on most platforms. This section details which these tools are, why they are needed, and how to install them.

Software environments: pixi or miniconda

The first step is ensuring you have an appropriate tool to manage your software environments. We highly recommend pixi because it is a fast and modern tool. Alternatively, you can use miniconda.

Modelblocks modules rely on Snakemake and conda during execution. Below are examples of how to install both tools using either pixi or miniconda.

Setting up a project with pixi

Follow the installation instructions on the pixi documentation.

Once installed:

# Create and open your project directory
pixi init my_project & cd my_project
# Install snakemake at the project level
pixi workspace channel add conda-forge bioconda
pixi add snakemake-minimal conda

Setting up a project with conda

Follow the installation instructions on the conda documentation. We recommend miniconda for a lightweight, minimal installation.

Once installed:

# Create and open your project directory
mkdir ./my_project & cd ./my_project
# Create a conda environment for your project
conda create -n my_project -c conda-forge -c bioconda --strict-channel-priority snakemake-minimal
conda activate my_project

Using modelblocks: Snakemake

You can import Modelblocks modules into your own Snakemake workflow using the module command. No other manual tool installation is required.

Creating a new Snakemake project?

To save time, you can setup your Snakemake project following a template. These offer standardised structures, which helps in maintainability.

If you are using pixi, we recommend using our own project template. If you are using miniconda, you can instead use the official Snakemake template. Instructions for either template are available in their respective repositories.

To start processing data with the module, you will need to interface with by configuring it, then providing input files (if needed), and requesting results. We explain how to do this in basic concepts.