:orphan: .. only available via index, not via toctree .. title:: Package Recipe 'confindr' .. highlight: bash confindr ======== .. conda:recipe:: confindr :replaces_section_title: :noindex: Detect intra\- and inter\-species bacterial contamination in NGS reads :homepage: https://github.com/OLC-Bioinformatics/ConFindr :documentation: https://OLC-Bioinformatics.github.io/ConFindr/ :license: MIT / MIT :recipe: /`confindr `_/`meta.yaml `_ .. conda:package:: confindr |downloads_confindr| |docker_confindr| :versions: .. raw:: html
0.8.1-10.8.1-00.7.4-00.7.3-00.7.2-00.7.1-00.7.0-10.7.0-00.6.0-0 ``0.8.1-1``,  ``0.8.1-0``,  ``0.7.4-0``,  ``0.7.3-0``,  ``0.7.2-0``,  ``0.7.1-0``,  ``0.7.0-1``,  ``0.7.0-0``,  ``0.6.0-0``,  ``0.5.1-0``,  ``0.5.0-0``,  ``0.4.8-0``,  ``0.4.7-0``,  ``0.4.6-0``,  ``0.4.5-0``,  ``0.4.4-0``,  ``0.4.3-0``,  ``0.4.2-0``,  ``0.4.1-0``,  ``0.4.0-0``,  ``0.3.4-0``,  ``0.3.3-0``,  ``0.3.2-0`` .. raw:: html
:depends bbmap: ``>=39.01`` :depends biopython: ``1.81.*`` :depends kma: ``>=1.4.9`` :depends mash: ``>=2.3`` :depends minimap2: :depends pysam: ``>=0.15`` :depends pytest: :depends python: ``>=3.9.15`` :depends samtools: ``>=1.6`` :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 confindr and update with:: mamba update confindr To create a new environment, run:: mamba create --name myenvname confindr 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/confindr: (see `confindr/tags`_ for valid values for ````) .. |downloads_confindr| image:: https://img.shields.io/conda/dn/bioconda/confindr.svg?style=flat :target: https://anaconda.org/bioconda/confindr :alt: (downloads) .. |docker_confindr| image:: https://quay.io/repository/biocontainers/confindr/status :target: https://quay.io/repository/biocontainers/confindr .. _`confindr/tags`: https://quay.io/repository/biocontainers/confindr?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/confindr/README.html) .. |install-with-bioconda| image:: https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat :target: http://bioconda.github.io/recipes/confindr/README.html