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biobb_pytorch

Introduction

biobb_pytorch is the Biobb module collection to create and train ML & DL models using the popular PyTorch Python library. Biobb (BioExcel building blocks) packages are Python building blocks that create new layer of compatibility and interoperability over popular bioinformatics tools. The latest documentation of this package can be found in our readthedocs site: latest API documentation.

Version

v4.2.0 2024.1

Installation

Using PIP:

Important: PIP only installs the package. All the dependencies must be installed separately. To perform a complete installation, please use ANACONDA, DOCKER or SINGULARITY.

Using ANACONDA:

Using DOCKER:

  • Installation:

      docker pull quay.io/biocontainers/biobb_pytorch:4.2.0--pyhad2cae4_0
    
  • Usage:

      docker run quay.io/biocontainers/biobb_pytorch:4.2.0--pyhad2cae4_0 <command>
    

Using SINGULARITY:

MacOS users: it’s strongly recommended to avoid Singularity and use Docker as containerization system.

  • Installation:

      singularity pull --name biobb_pytorch.sif https://depot.galaxyproject.org/singularity/biobb_pytorch:4.2.0--pyhad2cae4_0
    
  • Usage:

      singularity exec biobb_pytorch.sif <command>
    

The command list and specification can be found at the Command Line documentation.