:orphan: .. only available via index, not via toctree .. title:: Package Recipe 'pyscaf' .. highlight: bash pyscaf ====== .. conda:recipe:: pyscaf :replaces_section_title: :noindex: Genome assembly scaffolding using information from paired\-end\/mate\-pair libraries\, long reads\, and synteny to closely related species. :homepage: https://github.com/lpryszcz/pyScaf :license: GPL3 / GPLv3 :recipe: /`pyscaf `_/`meta.yaml `_ .. conda:package:: pyscaf |downloads_pyscaf| |docker_pyscaf| :versions: ``0.12a4-3``,  ``0.12a4-2``,  ``0.12a4-0`` :depends fastaindex: :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 pyscaf and update with:: mamba update pyscaf To create a new environment, run:: mamba create --name myenvname pyscaf 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/pyscaf: (see `pyscaf/tags`_ for valid values for ````) .. |downloads_pyscaf| image:: https://img.shields.io/conda/dn/bioconda/pyscaf.svg?style=flat :target: https://anaconda.org/bioconda/pyscaf :alt: (downloads) .. |docker_pyscaf| image:: https://quay.io/repository/biocontainers/pyscaf/status :target: https://quay.io/repository/biocontainers/pyscaf .. _`pyscaf/tags`: https://quay.io/repository/biocontainers/pyscaf?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/pyscaf/README.html) .. |install-with-bioconda| image:: https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat :target: http://bioconda.github.io/recipes/pyscaf/README.html