Metadata-Version: 1.1
Name: pnnl-atlas
Version: 1.0.31
Summary: ATLAS - a framework for assembly, annotation, and genomic binning of metagenomic and metatranscriptomic data
Home-page: https://github.com/pnnl/atlas
Author: Joe Brown
Author-email: joe.brown@pnnl.gov
License: MIT
Description-Content-Type: UNKNOWN
Description: ATLAS
        =====
        
        |DOI|
        
        .. image:: resources/images/atlas_workflow.png
        
        Documentation
        =============
        
        |Documentation Status|
        
        Install
        =======
        
        All dependencies are installed via
        `conda <https://www.continuum.io/downloads>`__ using the
        `bioconda <https://github.com/bioconda/bioconda-recipes>`__ channel. The
        workflow and some dependencies require Python 3.
        
        The intended usage requires ``conda``.
        
        Further dependencies will be installed on the first execution of the
        assembly or annotation protocol and re-used on subsequent executions of
        the protocols.
        
        For more information related to bioconda, see:
        https://bioconda.github.io/
        
        As a New Environment
        --------------------
        
        With ``conda``, execute:
        
        ::
        
            conda create -n atlas -c bioconda python=3.6 \
                snakemake bbmap=37.78 click ruamel.yaml
        
        Load the environment:
        
        ::
        
            source activate atlas
        
        Install ``atlas``:
        
        ::
        
            pip install -U pnnl-atlas
        
        In the Same Environment
        -----------------------
        
        ::
        
            conda install -c bioconda python=3.6 \
                snakemake bbmap=37.78 click ruamel.yaml
            pip install -U pnnl-atlas
        
        Getting Started
        ===============
        
        After installing, one needs to download the required databases and
        create a sample configuration file.
        
        Databases
        ---------
        
        To download the databases and their respective metadata databases:
        
        ::
        
            atlas download -o ~/databases
        
        The downloads use approximately 30 GB of disk space.
        
        Configuration File
        ------------------
        
        To create a configuration file run:
        
        ::
        
            atlas make-config --database-dir ~/databases \
                config.yaml ~/directory_with_fastqs
        
        Sample names and file paths along with default settings will populate
        config.yaml. This `YAML <http://www.yaml.org/start.html>`__ file can be
        updated with any text editor.
        
        Sample names should be A-Z characters and can be dash ("-") delimited.
        
        For complete documentation, please see: |Documentation Status|
        
        Assembly
        --------
        
        After editing your configuration file and adjusting any additional
        parameters we run assemblies across our samples using:
        
        ::
        
            atlas assemble config.yaml
        
        By default, this will write results into our current working directory
        across the total number of CPU cores available.
        
        License
        =======
        
        BSD-3.
        
        Disclaimer
        ==========
        
        This material was prepared as an account of work sponsored by an agency
        of the United States Government. Neither the United States Government
        nor the United States Department of Energy, nor Battelle, nor any of
        their employees, nor any jurisdiction or organization that has
        cooperated in the development of these materials, makes any warranty,
        express or implied, or assumes any legal liability or responsibility for
        the accuracy, completeness, or usefulness or any information, apparatus,
        product, software, or process disclosed, or represents that its use
        would not infringe privately owned rights.
        
        Reference herein to any specific commercial product, process, or service
        by trade name, trademark, manufacturer, or otherwise does not
        necessarily constitute or imply its endorsement, recommendation, or
        favoring by the United States Government or any agency thereof, or
        Battelle Memorial Institute. The views and opinions of authors expressed
        herein do not necessarily state or reflect those of the United States
        Government or any agency thereof.
        
        PACIFIC NORTHWEST NATIONAL LABORATORY operated by BATTELLE for the
        UNITED STATES DEPARTMENT OF ENERGY under Contract DE-AC05-76RL01830
        
        .. |DOI| image:: https://zenodo.org/badge/75199304.svg
           :target: https://zenodo.org/badge/latestdoi/75199304
        .. |Documentation Status| image:: https://readthedocs.org/projects/pnnl-atlas/badge/?version=latest
           :target: http://pnnl-atlas.readthedocs.io/en/latest/?badge=latest
        
Platform: UNKNOWN
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
