:orphan: .. only available via index, not via toctree .. title:: Package Recipe 'autometa' .. highlight: bash autometa ======== .. conda:recipe:: autometa :replaces_section_title: :noindex: Automated extraction of genomes from shotgun metagenomes :homepage: https://github.com/KwanLab/Autometa :documentation: https://autometa.readthedocs.io/en/latest/ :license: AGPL / AGPL-3.0 :recipe: /`autometa `_/`meta.yaml `_ An automated binning pipeline for metagenomes\, in particular host\-associated and highly complex ones. Miller\, I. J.\; Rees\, E. R.\; Ross\, J.\; Miller\, I.\; Baxa\, J.\; Lopera\, J.\; Kerby\, R. L.\; Rey\, F. E.\; Kwan\, J. C. Autometa\: Automated extraction of microbial genomes from individual shotgun metagenomes. Nucleic Acids Research\, 2019. DOI\: https\:\/\/doi.org\/10.1093\/nar\/gkz148 .. conda:package:: autometa |downloads_autometa| |docker_autometa| :versions: ``2.2.1-0``,  ``2.2.0-0``,  ``2.1.0-0``,  ``2.0.3-0``,  ``2.0.2-0``,  ``2.0.1-0``,  ``2.0.0-0`` :depends attrs: :depends bedtools: :depends biopython: :depends bowtie2: :depends diamond: ``>=2.0`` :depends gdown: :depends hmmer: :depends numba: ``>=0.47`` :depends numpy: ``>=1.13`` :depends pandas: ``>=1.1`` :depends parallel: :depends prodigal: ``>=2.5`` :depends python: ``>=3.7`` :depends requests: :depends rsync: :depends samtools: ``>=1.11`` :depends scikit-bio: :depends scikit-learn: ``>=1.3`` :depends scipy: :depends seqkit: :depends tqdm: :depends trimap: :depends tsne: :depends umap-learn: ``>=0.5`` :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 autometa and update with:: mamba update autometa To create a new environment, run:: mamba create --name myenvname autometa 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/autometa: (see `autometa/tags`_ for valid values for ````) .. |downloads_autometa| image:: https://img.shields.io/conda/dn/bioconda/autometa.svg?style=flat :target: https://anaconda.org/bioconda/autometa :alt: (downloads) .. |docker_autometa| image:: https://quay.io/repository/biocontainers/autometa/status :target: https://quay.io/repository/biocontainers/autometa .. _`autometa/tags`: https://quay.io/repository/biocontainers/autometa?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/autometa/README.html) .. |install-with-bioconda| image:: https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat :target: http://bioconda.github.io/recipes/autometa/README.html