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 7.15.2 (recommended)

      mamba create -c conda-forge -c bioconda -n snakemake snakemake=7.15.2

   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.

         # put this in your .bashrc profile
         export SNAKEMAKE_CONDA_PREFIX = path/to/conda/directory

      2. if you work on a cluster: configure the location of your cluster profile (i.e., the interface between Snakemake and your cluster's workload manager)

         # put this in your .bashrc profile
         export SNAKEMAKE_PROFILE = path/to/your/cluster/profile

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

   git clone git@github.com:user/{module}.git

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