Installation

Dependencies

To run metaGOflow you need to make sure you have the following set on your computing environment first:

• python3 [v 3.8+]

• Docker [v 19.+] or Singularity [v 3.7.+] / Apptainer [v 1.+]

• cwltool [v 3.+]

• rdflib [v 6.+]

• rdflib-jsonld [v 0.6.2]

• ro-crate-py [v 0.7.0]

• pyyaml [v 6.0]

• Node.js [v 10.24.0+]

• Available storage ~160GB for databases

You may either ensure you have those locally or you may use a conda environment we have built including them (conda_environment.yml, url).

On top of those, disk requirements need to be considered and depending on the analysis you are about to run they vary. Indicatively, you may have a look at the metaGOflow publication for computing resources used in various cases.

Installation

Get source code:

git clone https://github.com/emo-bon/MetaGOflow.git

Setup environment:

Get dependencies to run metaGOflow:

conda env create -f conda_environment.yml

This will create a conda environment called metagoflow. By running conda env list you will see your new environment. In case conda is not already installed on your computing system, you may follow the instructions to get it here.

In case Singularity runs fail with an error message mentioning that a .sif file is missing, you need to force-pull the images to be used from metaGOflow. To do so, you may run the get_singularity_images.sh [url] script that you shall find under the Installation folder.

Attention

Besides the database storage, metaGOflow requires a significant storage space during its performance. The final data products are a few megabytes, however maybe more than 1 TB might be needed during its run.