:orphan: .. only available via index, not via toctree .. title:: Package Recipe 'conterminator' .. highlight: bash conterminator ============= .. conda:recipe:: conterminator :replaces_section_title: :noindex: Conterminator\: software to detect contamination in large sequence sets :homepage: https://github.com/martin-steinegger/conterminator :license: GPL3 :recipe: /`conterminator `_/`meta.yaml `_ :links: doi: :doi:`10.1186/s13059-020-02023-1`, biotools: :biotools:`conterminator` .. conda:package:: conterminator |downloads_conterminator| |docker_conterminator| :versions: ``1.c74b5-1``,  ``1.c74b5-0`` :depends bzip2: ``>=1.0.8,<2.0a0`` :depends gawk: :depends libgcc-ng: ``>=9.3.0`` :depends libstdcxx-ng: ``>=9.3.0`` :depends openmp: :depends zlib: ``>=1.2.11,<1.3.0a0`` :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 conterminator and update with:: mamba update conterminator To create a new environment, run:: mamba create --name myenvname conterminator 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/conterminator: (see `conterminator/tags`_ for valid values for ````) .. |downloads_conterminator| image:: https://img.shields.io/conda/dn/bioconda/conterminator.svg?style=flat :target: https://anaconda.org/bioconda/conterminator :alt: (downloads) .. |docker_conterminator| image:: https://quay.io/repository/biocontainers/conterminator/status :target: https://quay.io/repository/biocontainers/conterminator .. _`conterminator/tags`: https://quay.io/repository/biocontainers/conterminator?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/conterminator/README.html) .. |install-with-bioconda| image:: https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat :target: http://bioconda.github.io/recipes/conterminator/README.html