:orphan: .. only available via index, not via toctree .. title:: Package Recipe 'sopa' .. highlight: bash sopa ==== .. conda:recipe:: sopa :replaces_section_title: :noindex: Spatial\-omics pipeline and analysis. :homepage: https://gustaveroussy.github.io/sopa :license: BSD / BSD-3-Clause :recipe: /`sopa `_/`meta.yaml `_ .. conda:package:: sopa |downloads_sopa| |docker_sopa| :versions: ``1.1.5-0`` :depends botocore: ``1.34.19.*`` :depends flake8: ``>=7.0.0,<8.0.0`` :depends python: ``>=3.9,<3.12`` :depends scanpy: ``>=1.9.8`` :depends spatialdata: ``>=0.2.0`` :depends spatialdata-io: ``>=0.1.3`` :depends typer: ``>=0.9.0`` :requirements: :additional platforms: .. 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 sopa and update with:: mamba update sopa To create a new environment, run:: mamba create --name myenvname sopa 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/sopa: (see `sopa/tags`_ for valid values for ````) .. |downloads_sopa| image:: https://img.shields.io/conda/dn/bioconda/sopa.svg?style=flat :target: https://anaconda.org/bioconda/sopa :alt: (downloads) .. |docker_sopa| image:: https://quay.io/repository/biocontainers/sopa/status :target: https://quay.io/repository/biocontainers/sopa .. _`sopa/tags`: https://quay.io/repository/biocontainers/sopa?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/sopa/README.html) .. |install-with-bioconda| image:: https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat :target: http://bioconda.github.io/recipes/sopa/README.html