pnnl-atlas 1.0.32

ATLAS

Documentation

Install

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/

conda create -n atlas -c bioconda python=3.6 \
    snakemake bbmap=37.78 click ruamel.yaml

source activate atlas

pip install -U pnnl-atlas

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.

atlas download -o ~/databases

atlas make-config --database-dir ~/databases \
    config.yaml ~/directory_with_fastqs

atlas assemble config.yaml

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.

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