pnnl-atlas 1.0.32
ATLAS - a framework for assembly, annotation, and genomic binning of metagenomic and metatranscriptomic data
License: MIT

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