:orphan: .. only available via index, not via toctree .. title:: Package Recipe 'agfusion' .. highlight: bash agfusion ======== .. conda:recipe:: agfusion :replaces_section_title: :noindex: Python package to annotate and visualize gene fusions. :homepage: https://github.com/murphycj/AGFusion :license: MIT / MIT :recipe: /`agfusion `_/`meta.yaml `_ :links: doi: :doi:`10.1101/080903` .. conda:package:: agfusion |downloads_agfusion| |docker_agfusion| :versions: ``1.252-1``,  ``1.252-0``,  ``1.251-0``,  ``1.231-0``,  ``1.23-0``,  ``1.4.1-0``,  ``1.2-2``,  ``1.2-0``,  ``1.0-0`` :depends biopython: ``>=1.67`` :depends future: ``>=0.16.0`` :depends matplotlib: ``>=1.5.0`` :depends nose2: ``>=0.6.5`` :depends pandas: ``>=0.18.1`` :depends pyensembl: ``>=1.1.0`` :depends python: :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 agfusion and update with:: mamba update agfusion To create a new environment, run:: mamba create --name myenvname agfusion 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/agfusion: (see `agfusion/tags`_ for valid values for ````) .. |downloads_agfusion| image:: https://img.shields.io/conda/dn/bioconda/agfusion.svg?style=flat :target: https://anaconda.org/bioconda/agfusion :alt: (downloads) .. |docker_agfusion| image:: https://quay.io/repository/biocontainers/agfusion/status :target: https://quay.io/repository/biocontainers/agfusion .. _`agfusion/tags`: https://quay.io/repository/biocontainers/agfusion?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/agfusion/README.html) .. |install-with-bioconda| image:: https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat :target: http://bioconda.github.io/recipes/agfusion/README.html