Installation

The following instructions should take less than 10 minutes to execute and hold true for any Snakemake workflow, including all MR.PARETO modules.

1. Install and setup Snakemake (only once)
   1. Install Snakemake, which requires conda and mamba, following the offical documentation (the full installation is recommended).

      conda install -n base -c conda-forge mamba
      conda activate base
      mamba create -c conda-forge -c bioconda -n snakemake snakemake

      Most modules were developed and tested with Snakemake version 8.20.1 (recommended).

      mamba create -c conda-forge -c bioconda -n snakemake snakemake=8.20.1

      In case you are using multiple Snakemake versions simultaneously, indicate the version in the environment name.

      mamba create -c conda-forge -c bioconda -n snakemake8_20_1 snakemake=8.20.1

   2. Set Snakemake environment variables for convenience (optional, but highly recommended).
      1. Configure a dedicated Snakemake conda environment folder (e.g., on a non-backed-up partition of your cluster) to avoid redundant installations and consolidate all conda environments installed by Snakemake in one easy-to-manage location.

         # add this to your ~/.bashrc profile
         export SNAKEMAKE_CONDA_PREFIX = path/to/conda/directory

      2. If you work on a cluster and/or want to set default command line arguments (CLI) you should create a global Snakemake profile. Configure the location of your global Snakemake profile, which serves as the interface between Snakemake and your cluster's workload manager (e.g., SLURM) and applies your predefined CLIs.

         # add this to your ~/.bashrc profile
         export SNAKEMAKE_PROFILE = path/to/your/cluster/profile

2. Clone the {module} repository (only once per module).

   git clone [email protected]:user/{module}.git

Note

All software dependencies are installed and managed automatically via Snakemake and conda/mamba. They are installed upon the first run of the module.