:orphan: .. only available via index, not via toctree .. title:: Package Recipe 'ngscheckmate' .. highlight: bash ngscheckmate ============ .. conda:recipe:: ngscheckmate :replaces_section_title: :noindex: Software package for identifying next generation sequencing \(NGS\) data files from the same individual. :homepage: https://github.com/parklab/NGSCheckMate :license: MIT :recipe: /`ngscheckmate `_/`meta.yaml `_ This version is built from a pull request which fixes a handful of known bugs. .. conda:package:: ngscheckmate |downloads_ngscheckmate| |docker_ngscheckmate| :versions: ``1.0.1-1``,  ``1.0.1-0``,  ``1.0.0-3``,  ``1.0.0-1``,  ``1.0.0-0`` :depends bcftools: :depends bowtie: :depends perl: ``>=5.32.1,<6.0a0 *_perl5`` :depends python: ``2.7.*`` :depends r-base: ``>=4.0,<4.1.0a0`` :depends samtools: :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 ngscheckmate and update with:: mamba update ngscheckmate To create a new environment, run:: mamba create --name myenvname ngscheckmate 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/ngscheckmate: (see `ngscheckmate/tags`_ for valid values for ````) .. |downloads_ngscheckmate| image:: https://img.shields.io/conda/dn/bioconda/ngscheckmate.svg?style=flat :target: https://anaconda.org/bioconda/ngscheckmate :alt: (downloads) .. |docker_ngscheckmate| image:: https://quay.io/repository/biocontainers/ngscheckmate/status :target: https://quay.io/repository/biocontainers/ngscheckmate .. _`ngscheckmate/tags`: https://quay.io/repository/biocontainers/ngscheckmate?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/ngscheckmate/README.html) .. |install-with-bioconda| image:: https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat :target: http://bioconda.github.io/recipes/ngscheckmate/README.html