:orphan: .. only available via index, not via toctree .. title:: Package Recipe 'cytoscape' .. highlight: bash cytoscape ========= .. conda:recipe:: cytoscape :replaces_section_title: :noindex: Cytoscape\: an open source platform for network analysis and visualization. :homepage: https://cytoscape.org :developer docs: https://github.com/cytoscape/cytoscape :license: GPL / LGPL :recipe: /`cytoscape `_/`meta.yaml `_ :links: biotools: :biotools:`cytoscape`, doi: :doi:`10.1101/gr.1239303` .. conda:package:: cytoscape |downloads_cytoscape| |docker_cytoscape| :versions: ``3.10.2-0``,  ``3.10.1-0``,  ``3.9.1-1``,  ``3.9.1-0``,  ``3.9.0-0``,  ``3.8.2-0``,  ``3.7.2-1``,  ``3.7.2-0``,  ``3.7.1-0`` :depends font-ttf-dejavu-sans-mono: :depends fontconfig: :depends freetype: :depends openjdk: ``>=17,<20`` :depends xorg-libxtst: :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 cytoscape and update with:: mamba update cytoscape To create a new environment, run:: mamba create --name myenvname cytoscape 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/cytoscape: (see `cytoscape/tags`_ for valid values for ````) .. |downloads_cytoscape| image:: https://img.shields.io/conda/dn/bioconda/cytoscape.svg?style=flat :target: https://anaconda.org/bioconda/cytoscape :alt: (downloads) .. |docker_cytoscape| image:: https://quay.io/repository/biocontainers/cytoscape/status :target: https://quay.io/repository/biocontainers/cytoscape .. _`cytoscape/tags`: https://quay.io/repository/biocontainers/cytoscape?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/cytoscape/README.html) .. |install-with-bioconda| image:: https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat :target: http://bioconda.github.io/recipes/cytoscape/README.html