:orphan: .. only available via index, not via toctree .. title:: Package Recipe 'pybel' .. highlight: bash pybel ===== .. conda:recipe:: pybel :replaces_section_title: :noindex: PyBEL is a Python package for parsing and handling biological networks encoded in the Biological Expression Language \(BEL\). :homepage: https://pybel.readthedocs.io :documentation: https://pybel.readthedocs.io/en/latest/ :developer docs: https://github.com/pybel/pybel :license: APACHE / Apache-2.0 :recipe: /`pybel `_/`meta.yaml `_ :links: doi: :doi:`10.1093/bioinformatics/btx660` .. conda:package:: pybel |downloads_pybel| |docker_pybel| :versions: ``0.13.2-0``,  ``0.9.3-1``,  ``0.9.3-0``,  ``0.5.4-0``,  ``0.4.0-0`` :depends bel-resources: :depends click: :depends click-plugins: :depends networkx: ``>=2.1`` :depends pyparsing: :depends python: ``>=3.5`` :depends requests: :depends requests-file: :depends sqlalchemy: :depends tqdm: :requirements: .. rubric:: Installation You need a conda-compatible package manager (currently either `micromamba `_, `mamba `_, or `conda `_) and the Bioconda channel already activated (see :ref:`set-up-channels`). While any of above package managers is fine, it is currently recommended to use either micromamba or mamba (see `here `_ for installation instructions). We will show all commands using mamba below, but the arguments are the same for the two others. Given that you already have a conda environment in which you want to have this package, install with:: mamba install pybel and update with:: mamba update pybel To create a new environment, run:: mamba create --name myenvname pybel with ``myenvname`` being a reasonable name for the environment (see e.g. the `mamba docs `_ for details and further options). Alternatively, use the docker container:: docker pull quay.io/biocontainers/pybel: (see `pybel/tags`_ for valid values for ````) .. |downloads_pybel| image:: https://img.shields.io/conda/dn/bioconda/pybel.svg?style=flat :target: https://anaconda.org/bioconda/pybel :alt: (downloads) .. |docker_pybel| image:: https://quay.io/repository/biocontainers/pybel/status :target: https://quay.io/repository/biocontainers/pybel .. _`pybel/tags`: https://quay.io/repository/biocontainers/pybel?tab=tags .. raw:: html Download stats ----------------- .. raw:: html :file: ../../templates/package_dashboard.html Link to this page ----------------- Render an |install-with-bioconda| badge with the following MarkDown:: [![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io/recipes/pybel/README.html) .. |install-with-bioconda| image:: https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat :target: http://bioconda.github.io/recipes/pybel/README.html