Getting Started

Prerequisites

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Make sure you have a working installation of conda or mamba (recommended)

Clone and navigate into the repository:

   git clone https://github.com/aweich/VIS
   cd VIS

Setting up the Environment

You have two options for setting up the pipeline:

The pipeline contains the option for an integrated package management functionality. In other words, the workflow will be installing all required packages for each rule as needed. This means that we only need to install a lightweight environment ourselves to run the pipeline locally.

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While the traditional method of setting up the pipeline offers the advantage of being lightweight in its package installation, the actual execution of the pipeline can be slightly more complex and may require additional adjustments based on your local setup of conda or mamba. To address this, we also provide a convenient alternative that installs all required packages for the pipeline within a single environment below.

Create the minimal environment for running the pipeline: 

    mamba env create --name VIS_minimal -f workflow/envs/VIS_minimal_env.yml

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You can use conda instead of mamba if desired, but mamba is faster.

Then, activate the environment: 

   conda activate VIS_minimal
2. Alternative

Snakemake also allows us to use a single environment throughout the whole pipeline. We can also make use of that to create a convenient alternative for the setup of the pipeline. Depending on your system, this might make the downsteam execution of the workflow overall more convenient.

Create the full environment for running the pipeline:

   mamba env create --name VIS_full -f workflow/envs/VIS_full_env.yml

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It is also possible to use conda for the creation of the environment. Since we are installing more dependencies here, the use of mamba is highly encouraged.

Then, activate the environment:

   conda activate VIS_full