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biobb_io

Introduction

Biobb_io is the Biobb module collection to fetch data to be consumed by the rest of the Biobb building blocks. 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

v4.1.0 2023.3

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_io:4.1.0--pyhdfd78af_0
    
  • Usage:

      docker run quay.io/biocontainers/biobb_io:4.1.0--pyhdfd78af_0 <command>
    

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

Using SINGULARITY:

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

  • Installation:

      singularity pull --name biobb_io.sif https://depot.galaxyproject.org/singularity/biobb_io:4.1.0--pyhdfd78af_0
    
  • Usage:

      singularity exec biobb_io.sif <command>
    

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