FAIRsoft 0.1.14

FAIRsoft package for the aggregation of Life Sciences software metadata and FAIR evaluation.

FAIRsoft

Library for the aggregation of Life Sciences software metadata and FAIR evaluation.

Installation

Install using pip:

pip install FAIRsoft

Requirements

In order to use the Bioconda and repositories (GitHub and Bitbucket) importers, the following two tools need to be installed:

• bioconda-utils is required by the bioconda importer.

  bioconda-utils is a bioconda package and thus requires Conda.

  :exclamation: The large size of bioconda-utils package can cause Conda to crash during the installation process. Using Mamba instead of Conda prevents this problem.

  :exclamation: bioconda-utils requires Python 3.7 or lower. Simulating a compatible platform might be necessary. To do so, use the following commands:

  # create the environment
  mamba create -n myenv
  
  # activate the environment
  conda activate myenv
  
  # before installing anything in the environment, set the usage of x86_64 architecture
  conda config --env --set subdir osx-64
  

• opeb-enrichers/repoEnricher is required by the Source Code Respositories importer.

• AnyStyle is required by the Galaxy Toolshed importer.

Usage

Example of usage in this jupyter-notebook.

Docker images for importation, transformation and integration

Given the complexity of the requirements installation process, it is highly recommended to use the dockerized version of the different importers, as well as the transformation and integration steps.

They are available in the following repositories. Instructions on how to configure them can be found in their respective READMEs.

Importers:

• Bioconda importer
• Bioconductor importer
• Galaxy Toolshed importer
• OpenEBench tools importer
• OpenEBench metrics importer
• Sourceforge importer
• Repositories importer

Transformation:

• Transformation

Integration:

• Integration