:orphan: .. only available via index, not via toctree .. title:: Package Recipe 'metagenome-atlas' .. highlight: bash metagenome-atlas ================ .. conda:recipe:: metagenome-atlas :replaces_section_title: :noindex: ATLAS \- Three commands to start analysing your metagenome data :homepage: https://github.com/metagenome-atlas :documentation: https://metagenome-atlas.rtfd.io :developer docs: https://github.com/metagenome-atlas/atlas :license: BSD / BSD-3-Clause :recipe: /`metagenome-atlas `_/`meta.yaml `_ :links: doi: :doi:`10.1101/737528` Atlas is a easy to use metagenomic pipeline \# Quick Start Three commands to start analysing your metagenome data\: \`\`\` mamba install \-c bioconda \-c conda\-forge metagenome\-atlas atlas init \-\-db\-dir databases path\/to\/fastq\/files atlas run \`\`\` All databases and dependencies are installed on the fly in the directory \`db\-dir\`. You want to run these three commands on the example\_data on the GitHub repo. If you have more time\, then we recommend you configure atlas according to your needs. \- check the \`samples.tsv\` \- edit the \`config.yaml\` \- run atlas on any cluster system For more details see documentation. .. conda:package:: metagenome-atlas |downloads_metagenome-atlas| |docker_metagenome-atlas| :versions: .. raw:: html
2.18.1-02.18.0-02.17.2-02.17.1-02.17.0-02.16.3-02.16.2-02.16.1-02.15.2-0 ``2.18.1-0``,  ``2.18.0-0``,  ``2.17.2-0``,  ``2.17.1-0``,  ``2.17.0-0``,  ``2.16.3-0``,  ``2.16.2-0``,  ``2.16.1-0``,  ``2.15.2-0``,  ``2.15.1-0``,  ``2.15.0-0``,  ``2.14.3-0``,  ``2.14.2-0``,  ``2.14.0-0``,  ``2.13.1-0``,  ``2.13.0-0``,  ``2.12.0-1``,  ``2.12.0-0``,  ``2.11.1-0``,  ``2.11.0-1``,  ``2.11.0-0``,  ``2.10.0-0``,  ``2.9.1-0``,  ``2.9.0-0``,  ``2.8.2-0``,  ``2.8.1-0``,  ``2.8.0-0``,  ``2.7.0-0``,  ``2.6a4-0``,  ``2.6a2-0``,  ``2.6a1-0``,  ``2.5.0-0``,  ``2.4.5-0``,  ``2.4.4-0``,  ``2.4.3-0``,  ``2.4.2-0``,  ``2.4.1-0``,  ``2.4-0``,  ``2.3.5-0``,  ``2.3.4-0``,  ``2.3.3-0``,  ``2.3.2-0``,  ``2.3.beta2-0``,  ``2.2.0-0``,  ``2.1.4-1``,  ``2.1.4-0``,  ``2.1.3-0``,  ``2.1.1-0``,  ``2.0.6-1``,  ``2.0.5-1``,  ``2.0.4-1``,  ``2.0.3-1``,  ``2.0.1-1``,  ``2.0.1-0`` .. raw:: html
:depends bbmap: ``>=39.01,<40`` :depends click: ``>=7`` :depends cookiecutter: :depends graphviz: :depends mamba: :depends networkx: :depends numpy: ``1.21.*`` :depends pandas: ``>=1.2,<1.5`` :depends pathlib: :depends pyarrow: ``>=8`` :depends pygments: :depends python: ``>=3.8,<3.11`` :depends ruamel.yaml: ``>=0.17`` :depends snakemake-minimal: ``>=7.18.1,<7.26`` :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 metagenome-atlas and update with:: mamba update metagenome-atlas To create a new environment, run:: mamba create --name myenvname metagenome-atlas 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/metagenome-atlas: (see `metagenome-atlas/tags`_ for valid values for ````) .. |downloads_metagenome-atlas| image:: https://img.shields.io/conda/dn/bioconda/metagenome-atlas.svg?style=flat :target: https://anaconda.org/bioconda/metagenome-atlas :alt: (downloads) .. |docker_metagenome-atlas| image:: https://quay.io/repository/biocontainers/metagenome-atlas/status :target: https://quay.io/repository/biocontainers/metagenome-atlas .. _`metagenome-atlas/tags`: https://quay.io/repository/biocontainers/metagenome-atlas?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/metagenome-atlas/README.html) .. |install-with-bioconda| image:: https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat :target: http://bioconda.github.io/recipes/metagenome-atlas/README.html