:orphan: .. only available via index, not via toctree .. title:: Package Recipe 'mashmap' .. highlight: bash mashmap ======= .. conda:recipe:: mashmap :replaces_section_title: :noindex: A fast approximate aligner for long DNA sequences. :homepage: https://github.com/marbl/MashMap :license: Custom :recipe: /`mashmap `_/`meta.yaml `_ .. conda:package:: mashmap |downloads_mashmap| |docker_mashmap| :versions: .. raw:: html
3.1.3-03.1.2-03.1.1-03.1.0-03.0.6-03.0.5-03.0.4-03.0.2-03.0.1-1 ``3.1.3-0``,  ``3.1.2-0``,  ``3.1.1-0``,  ``3.1.0-0``,  ``3.0.6-0``,  ``3.0.5-0``,  ``3.0.4-0``,  ``3.0.2-0``,  ``3.0.1-1``,  ``3.0.1-0``,  ``3.0-0``,  ``2.0-8``,  ``2.0-7``,  ``2.0-6``,  ``2.0-5``,  ``2.0-4``,  ``2.0-3``,  ``2.0-2``,  ``2.0-1``,  ``2.0-0``,  ``1.0-1``,  ``1.0-0`` .. raw:: html
:depends gsl: ``>=2.7,<2.8.0a0`` :depends htslib: ``>=1.19,<1.20.0a0`` :depends libgcc-ng: ``>=12`` :depends libstdcxx-ng: ``>=12`` :depends libzlib: ``>=1.2.13,<1.3.0a0`` :depends openblas: :depends zlib: :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 mashmap and update with:: mamba update mashmap To create a new environment, run:: mamba create --name myenvname mashmap 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/mashmap: (see `mashmap/tags`_ for valid values for ````) .. |downloads_mashmap| image:: https://img.shields.io/conda/dn/bioconda/mashmap.svg?style=flat :target: https://anaconda.org/bioconda/mashmap :alt: (downloads) .. |docker_mashmap| image:: https://quay.io/repository/biocontainers/mashmap/status :target: https://quay.io/repository/biocontainers/mashmap .. _`mashmap/tags`: https://quay.io/repository/biocontainers/mashmap?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/mashmap/README.html) .. |install-with-bioconda| image:: https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat :target: http://bioconda.github.io/recipes/mashmap/README.html