All dependencies are installed via conda using the bioconda 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/

With conda, execute:

conda create -n atlas -c bioconda -c conda-forge python>=3.6 snakemake pandas bbmap=37.78 click ruamel.yaml biopython

Load the environment:

source activate atlas

Install atlas:

pip install -U pnnl-atlas

or install the up to date atlas from github:

git clone https://github.com/pnnl/atlas.git
cd atlas
pip install .

After installing, one needs to download the required databases and create a sample configuration file.

To download the databases and their respective metadata databases:

atlas download -o ~/databases

The downloads use approximately 100 GB of disk space.

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 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:

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.

BSD-3.

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