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    "info": {
        "author": "Joe Brown",
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        "description": "ATLAS\n=====\n\n|DOI|\n\n.. image:: resources/images/atlas_workflow.png\n\nDocumentation\n=============\n\n|Documentation Status|\n\nInstall\n=======\n\nAll dependencies are installed via\n`conda <https://www.continuum.io/downloads>`__ using the\n`bioconda <https://github.com/bioconda/bioconda-recipes>`__ channel. The\nworkflow and some dependencies require Python 3.\n\nThe intended usage requires ``conda``.\n\nFurther dependencies will be installed on the first execution of the\nassembly or annotation protocol and re-used on subsequent executions of\nthe protocols.\n\nFor more information related to bioconda, see:\nhttps://bioconda.github.io/\n\nAs a New Environment\n--------------------\n\nWith ``conda``, execute:\n\n::\n\n    conda create -n atlas -c bioconda python=3.6 \\\n        snakemake bbmap=37.78 click ruamel.yaml\n\nLoad the environment:\n\n::\n\n    source activate atlas\n\nInstall ``atlas``:\n\n::\n\n    pip install -U pnnl-atlas\n\nIn the Same Environment\n-----------------------\n\n::\n\n    conda install -c bioconda python=3.6 \\\n        snakemake bbmap=37.78 click ruamel.yaml\n    pip install -U pnnl-atlas\n\nGetting Started\n===============\n\nAfter installing, one needs to download the required databases and\ncreate a sample configuration file.\n\nDatabases\n---------\n\nTo download the databases and their respective metadata databases:\n\n::\n\n    atlas download -o ~/databases\n\nThe downloads use approximately 30 GB of disk space.\n\nConfiguration File\n------------------\n\nTo create a configuration file run:\n\n::\n\n    atlas make-config --database-dir ~/databases \\\n        config.yaml ~/directory_with_fastqs\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\nupdated with any text editor.\n\nSample names should be A-Z characters and can be dash (\"-\") delimited.\n\nFor complete documentation, please see: |Documentation Status|\n\nAssembly\n--------\n\nAfter editing your configuration file and adjusting any additional\nparameters we run assemblies across our samples using:\n\n::\n\n    atlas assemble config.yaml\n\nBy default, this will write results into our current working directory\nacross the total number of CPU cores available.\n\nLicense\n=======\n\nBSD-3.\n\nDisclaimer\n==========\n\nThis material was prepared as an account of work sponsored by an agency\nof the United States Government. Neither the United States Government\nnor the United States Department of Energy, nor Battelle, nor any of\ntheir employees, nor any jurisdiction or organization that has\ncooperated in the development of these materials, makes any warranty,\nexpress or implied, or assumes any legal liability or responsibility for\nthe accuracy, completeness, or usefulness or any information, apparatus,\nproduct, software, or process disclosed, or represents that its use\nwould not infringe privately owned rights.\n\nReference herein to any specific commercial product, process, or service\nby trade name, trademark, manufacturer, or otherwise does not\nnecessarily constitute or imply its endorsement, recommendation, or\nfavoring by the United States Government or any agency thereof, or\nBattelle Memorial Institute. The views and opinions of authors expressed\nherein do not necessarily state or reflect those of the United States\nGovernment or any agency thereof.\n\nPACIFIC NORTHWEST NATIONAL LABORATORY operated by BATTELLE for the\nUNITED STATES DEPARTMENT OF ENERGY under Contract DE-AC05-76RL01830\n\n.. |DOI| image:: https://zenodo.org/badge/75199304.svg\n   :target: https://zenodo.org/badge/latestdoi/75199304\n.. |Documentation Status| image:: https://readthedocs.org/projects/pnnl-atlas/badge/?version=latest\n   :target: http://pnnl-atlas.readthedocs.io/en/latest/?badge=latest\n\n\n",
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        "name": "pnnl-atlas",
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        "summary": "ATLAS - a framework for assembly, annotation, and genomic binning of metagenomic and metatranscriptomic data",
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