:orphan: .. only available via index, not via toctree .. title:: Package Recipe 'cytocad' .. highlight: bash cytocad ======= .. conda:recipe:: cytocad :replaces_section_title: :noindex: Large copy\-number variation detector with low\-depth whole\-genome sequencing data :homepage: https://github.com/cytham/cytocad :license: GPL3 / GPL-3.0-or-later :recipe: /`cytocad `_/`meta.yaml `_ .. conda:package:: cytocad |downloads_cytocad| |docker_cytocad| :versions: ``1.0.3-2``,  ``1.0.3-1``,  ``1.0.3-0``,  ``1.0.2-0``,  ``1.0.1-0`` :depends bedtools: ``>=2.26.0`` :depends libgcc-ng: ``>=12`` :depends librsvg: ``>=2.50.3`` :depends matplotlib-base: ``>=2.2.3`` :depends numpy: ``>=1.17.3`` :depends pybedtools: ``>=0.8.0`` :depends pysam: ``>=0.15.3`` :depends python: ``>=3.10,<3.11.0a0`` :depends python_abi: ``3.10.* *_cp310`` :depends ruptures: ``>=1.1.3`` :depends samtools: ``>=1.3`` :depends scipy: ``>=1.2.1`` :depends tagore: ``>=1.1.0`` :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 cytocad and update with:: mamba update cytocad To create a new environment, run:: mamba create --name myenvname cytocad 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/cytocad: (see `cytocad/tags`_ for valid values for ````) .. |downloads_cytocad| image:: https://img.shields.io/conda/dn/bioconda/cytocad.svg?style=flat :target: https://anaconda.org/bioconda/cytocad :alt: (downloads) .. |docker_cytocad| image:: https://quay.io/repository/biocontainers/cytocad/status :target: https://quay.io/repository/biocontainers/cytocad .. _`cytocad/tags`: https://quay.io/repository/biocontainers/cytocad?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/cytocad/README.html) .. |install-with-bioconda| image:: https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat :target: http://bioconda.github.io/recipes/cytocad/README.html