:orphan: .. only available via index, not via toctree .. title:: Package Recipe 'desman' .. highlight: bash desman ====== .. conda:recipe:: desman :replaces_section_title: :noindex: De novo Extraction of Strains from MetAgeNomes :homepage: https://github.com/chrisquince/DESMAN :license: BSD / BSD :recipe: /`desman `_/`meta.yaml `_ :links: doi: :doi:`10.1186/s13059-017-1309-9` .. conda:package:: desman |downloads_desman| |docker_desman| :versions: ``2.1-8``,  ``2.1-7``,  ``2.1-6``,  ``2.1-4``,  ``2.1-3``,  ``2.1-2``,  ``2.1-1``,  ``2.1-0`` :depends bcbio-gff: :depends biopython: :depends cython: ``>=0.19.1`` :depends gsl: ``>=2.7,<2.8.0a0`` :depends libgcc-ng: ``>=12`` :depends numpy: ``>=1.21.6,<2.0a0`` :depends pandas: ``>=0.11.0`` :depends pysam: :depends python: ``>=3.10,<3.11.0a0`` :depends python_abi: ``3.10.* *_cp310`` :depends r-getopt: :depends r-ggplot2: ``>=2.2.2`` :depends r-labeling: :depends r-reshape: ``>=0.8.7`` :depends scikit-learn: :depends scipy: ``>=0.12.0`` :depends setuptools: :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 desman and update with:: mamba update desman To create a new environment, run:: mamba create --name myenvname desman 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/desman: (see `desman/tags`_ for valid values for ````) .. |downloads_desman| image:: https://img.shields.io/conda/dn/bioconda/desman.svg?style=flat :target: https://anaconda.org/bioconda/desman :alt: (downloads) .. |docker_desman| image:: https://quay.io/repository/biocontainers/desman/status :target: https://quay.io/repository/biocontainers/desman .. _`desman/tags`: https://quay.io/repository/biocontainers/desman?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/desman/README.html) .. |install-with-bioconda| image:: https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat :target: http://bioconda.github.io/recipes/desman/README.html