:orphan: .. only available via index, not via toctree .. title:: Package Recipe 'khmer' .. highlight: bash khmer ===== .. conda:recipe:: khmer :replaces_section_title: :noindex: khmer k\-mer counting library :homepage: https://khmer.readthedocs.io/ :developer docs: https://github.com/dib-lab/khmer :license: BSD / BSD License :recipe: /`khmer `_/`meta.yaml `_ :links: biotools: :biotools:`khmer`, doi: :doi:`10.12688/f1000research.6924.1` .. conda:package:: khmer |downloads_khmer| |docker_khmer| :versions: .. raw:: html
3.0.0a3-33.0.0a3-23.0.0a3-13.0.0a3-03.0.0a2-13.0.0a2-03.0.0a1-02.1.2-02.1-0 ``3.0.0a3-3``,  ``3.0.0a3-2``,  ``3.0.0a3-1``,  ``3.0.0a3-0``,  ``3.0.0a2-1``,  ``3.0.0a2-0``,  ``3.0.0a1-0``,  ``2.1.2-0``,  ``2.1-0``,  ``2.1rc1-0``,  ``2.0-2``,  ``2.0-1``,  ``2.0-0`` .. raw:: html
:depends _openmp_mutex: ``>=4.5`` :depends bz2file: :depends bzip2: ``>=1.0.8,<2.0a0`` :depends libgcc-ng: ``>=10.3.0`` :depends libstdcxx-ng: ``>=10.3.0`` :depends libzlib: ``>=1.2.11,<1.3.0a0`` :depends python: ``>=3.6,<3.7.0a0`` :depends python_abi: ``3.6.* *_cp36m`` :depends screed: ``>=1.0`` :depends zlib: ``>=1.2.11,<1.3.0a0`` :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 khmer and update with:: mamba update khmer To create a new environment, run:: mamba create --name myenvname khmer 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/khmer: (see `khmer/tags`_ for valid values for ````) .. |downloads_khmer| image:: https://img.shields.io/conda/dn/bioconda/khmer.svg?style=flat :target: https://anaconda.org/bioconda/khmer :alt: (downloads) .. |docker_khmer| image:: https://quay.io/repository/biocontainers/khmer/status :target: https://quay.io/repository/biocontainers/khmer .. _`khmer/tags`: https://quay.io/repository/biocontainers/khmer?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/khmer/README.html) .. |install-with-bioconda| image:: https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat :target: http://bioconda.github.io/recipes/khmer/README.html