:orphan: .. only available via index, not via toctree .. title:: Package Recipe 'bwakit' .. highlight: bash bwakit ====== .. conda:recipe:: bwakit :replaces_section_title: :noindex: A self\-consistent installation\-free package of scripts and precompiled binaries\, providing an end\-to\-end solution to read mapping :homepage: https://github.com/lh3/bwa/tree/master/bwakit :license: GPLv3 :recipe: /`bwakit `_/`meta.yaml `_ .. conda:package:: bwakit |downloads_bwakit| |docker_bwakit| :versions: ``0.7.17.dev1-1``,  ``0.7.17.dev1-0``,  ``0.7.15-3``,  ``0.7.15-2``,  ``0.7.15-1``,  ``0.7.15-0``,  ``0.7.12-0`` :depends bwa: ``0.7.17`` :depends fermi2: ``r170`` :depends htsbox: ``r315`` :depends k8: :depends perl: :depends ropebwt2: ``r187`` :depends samblaster: ``0.1.20`` :depends samtools: ``>=1.3`` :depends seqtk: ``r82`` :depends trimadap: ``r2`` :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 bwakit and update with:: mamba update bwakit To create a new environment, run:: mamba create --name myenvname bwakit 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/bwakit: (see `bwakit/tags`_ for valid values for ````) .. |downloads_bwakit| image:: https://img.shields.io/conda/dn/bioconda/bwakit.svg?style=flat :target: https://anaconda.org/bioconda/bwakit :alt: (downloads) .. |docker_bwakit| image:: https://quay.io/repository/biocontainers/bwakit/status :target: https://quay.io/repository/biocontainers/bwakit .. _`bwakit/tags`: https://quay.io/repository/biocontainers/bwakit?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/bwakit/README.html) .. |install-with-bioconda| image:: https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat :target: http://bioconda.github.io/recipes/bwakit/README.html