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    "info": {
        "author": "Joe Brown, Silas Kieser",
        "author_email": "brwnjm@gmail.com, silas.kieser@gmail.com",
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        "classifiers": [
            "Topic :: Scientific/Engineering :: Bio-Informatics"
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        "description": "# ATLAS\n\n[![DOI](https://zenodo.org/badge/75199304.svg)](https://zenodo.org/badge/latestdoi/75199304)\n\n[![Gitter chat](https://badges.gitter.im/pnnl-atlas/Lobby.png)](https://gitter.im/pnnl-atlas/Lobby)\n\n\n![scheme of workflow](resources/images/atlas_workflow.png)\n\n\n# Documentation\n\n[![Documentation Status](https://readthedocs.org/projects/metagenome-atlas/badge/?version=latest)](https://metagenome-atlas.readthedocs.io/en/latest/?badge=latest)\n\n# Install\n\nAll dependencies are installed via [conda](https://www.continuum.io/downloads) using the [bioconda](https://github.com/bioconda/bioconda-recipes) channel.\nThe workflow and some dependencies require Python 3.\n\nThe intended usage requires `conda`.\n\nFurther dependencies will be installed on the first execution of the assembly\nor annotation protocol and re-used on subsequent executions of the protocols.\n\nFor more information related to bioconda, see: https://bioconda.github.io/\n\n## As a New Environment\n\nWith `conda`, execute:\n\n```\nconda create -n atlas -c bioconda -c conda-forge python>=3.6 snakemake pandas bbmap=37.78 click ruamel.yaml biopython\n```\n\nLoad the environment:\n\n```\nsource activate atlas\n```\n\nInstall `atlas`:\n\n```\npip install -U metagenome-atlas\n```\n\nor install the up to date atlas from github:\n```\ngit clone https://github.com/metagenome-atlas/atlas.git\ncd atlas\npip install .\n```\n\n\n# Getting Started\n\nAfter installing, one needs to download the required databases and create a sample configuration file.\n\n\n## Databases\n\nTo download the databases and their respective metadata databases:\n\n```\natlas download -o ~/databases\n```\n\nThe downloads use approximately 100 GB of disk space.\n\n\n## Configuration File\n\nTo create a configuration file run:\n\n```\natlas make-config --database-dir ~/databases config.yaml ~/directory_with_fastqs\n```\n\nSample names and file paths along with default settings will populate\nconfig.yaml. This [YAML](http://www.yaml.org/start.html) file can be updated\nwith any text editor.\n\nSample names should be A-Z characters and can be dash (\"-\") delimited.\n\nFor complete documentation, please see: [![Documentation Status](https://readthedocs.org/projects/metagenome-atlas/badge/?version=latest)](https://metagenome-atlas.readthedocs.io/en/latest/?badge=latest)\n\n\n## Assembly\n\nAfter editing your configuration file and adjusting any additional parameters\nwe run assemblies across our samples using:\n\n```\natlas assemble config.yaml\n```\n\nBy default, this will write results into our current working directory across\nthe total number of CPU cores available.\n\n# License\n\nBSD-3.\n\n# Disclaimer\n\nThis material was prepared as an account of work sponsored by an agency of the\nUnited States Government.  Neither the United States Government nor the United\nStates Department of Energy, nor Battelle, nor any of their employees, nor any\njurisdiction or organization that has cooperated in the development of these\nmaterials, makes any warranty, express or implied, or assumes any legal\nliability or responsibility for the accuracy, completeness, or usefulness or\nany information, apparatus, product, software, or process disclosed, or\nrepresents that its use would not infringe privately owned rights.\n\nReference herein to any specific commercial product, process, or service by\ntrade name, trademark, manufacturer, or otherwise does not necessarily\nconstitute or imply its endorsement, recommendation, or favoring by the United\nStates Government or any agency thereof, or Battelle Memorial Institute. The\nviews and opinions of authors expressed herein do not necessarily state or\nreflect those of the United States Government or any agency thereof.\n\nPACIFIC NORTHWEST NATIONAL LABORATORY operated by BATTELLE for the UNITED\nSTATES DEPARTMENT OF ENERGY under Contract DE-AC05-76RL01830\n\n\n",
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        "name": "metagenome-atlas",
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