Installation

SCORPiOs is implemented as a Snakemake pipeline. Snakemake is a python-based language to build scalable and reproducible workflows. We take advantage of Snakemake’s integration with the package manager Conda to ship all SCORPiOs dependencies. The following instructions will help you get a running copy of the pipeline and set up your environnement.

Installing conda

The Conda package management system manages all SCORPiOs dependencies, including python packages and other software.

To install Conda:

  • Download Miniconda3 installer for your system here

  • Run the installation script: bash Miniconda3-latest-Linux-x86_64.sh or bash Miniconda3-latest-MacOSX-x86_64.sh, and accept the defaults

  • Open a new terminal, run conda update conda and press y to confirm updates

Installing SCORPiOs

  • Clone the repository:

git clone https://github.com/DyogenIBENS/SCORPIOS.git

  • Go to SCORPiOs root folder:

cd SCORPIOS

  • Create the main conda environment. We recommend using Mamba for a faster installation:

conda install -c conda-forge mamba
mamba env create -f envs/scorpios.yaml

  • Alternatively, you can use conda directly:

conda env create -f envs/scorpios.yaml

Note

Once the conda environnment is successfully created, the installation process is complete. You can proceed to the next section and test your installation on example data. Before running SCORPiOs, remember to activate the conda environment with conda activate scorpios.

Updating SCORPiOs conda environment

  • As of SCORPiOs v2.0.0, the conda environment was updated and needs to be reinstalled for users who have a previous version:

conda env remove --name scorpios
mamba env create -f envs/scorpios.yaml

Reference

  • Snakemake: Köster and Rahmann (2012) Snakemake - A scalable bioinformatics workflow engine. Bioinformatics, 28, 2520–2522.