:orphan: .. only available via index, not via toctree .. title:: Package Recipe 'bio_assembly_refinement' .. highlight: bash bio_assembly_refinement ======================= .. conda:recipe:: bio_assembly_refinement :replaces_section_title: :noindex: Assembly refinement tools\, mostly useful for \(but not limited to\) pacbio bacterial assemblies :homepage: https://github.com/nds/bio_assembly_refinement :license: GPLv3 :recipe: /`bio_assembly_refinement `_/`meta.yaml `_ .. conda:package:: bio_assembly_refinement |downloads_bio_assembly_refinement| |docker_bio_assembly_refinement| :versions: ``0.5.1-2``,  ``0.5.1-1``,  ``0.5.1-0``,  ``0.5.0-1``,  ``0.5.0-0`` :depends pyfastaq: ``>=3.10.0`` :depends pymummer: :depends python: ``>=3`` :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 bio_assembly_refinement and update with:: mamba update bio_assembly_refinement To create a new environment, run:: mamba create --name myenvname bio_assembly_refinement 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/bio_assembly_refinement: (see `bio_assembly_refinement/tags`_ for valid values for ````) .. |downloads_bio_assembly_refinement| image:: https://img.shields.io/conda/dn/bioconda/bio_assembly_refinement.svg?style=flat :target: https://anaconda.org/bioconda/bio_assembly_refinement :alt: (downloads) .. |docker_bio_assembly_refinement| image:: https://quay.io/repository/biocontainers/bio_assembly_refinement/status :target: https://quay.io/repository/biocontainers/bio_assembly_refinement .. _`bio_assembly_refinement/tags`: https://quay.io/repository/biocontainers/bio_assembly_refinement?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/bio_assembly_refinement/README.html) .. |install-with-bioconda| image:: https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat :target: http://bioconda.github.io/recipes/bio_assembly_refinement/README.html