All dependencies are installed via conda using the bioconda channel. The workflow and some dependencies require Python 3.5:

conda install python=3.5 snakemake

The intended usage requires conda.

Using Python 3.5, install atlas:

pip install -U pnnl-atlas

Following install, atlas should be executable:

$ atlas -h
Usage: atlas [OPTIONS] COMMAND [ARGS]...


  --version   Show the version and exit.
  -h, --help  Show this message and exit.

  assemble      assembly workflow
  download      download reference files
  make-config   prepopulate a configuration file with samples and defaults

Execution Environment

As ATLAS executes rules to generate output files, an environment is created using snakemake --use-conda in the background. No dependencies aside from python 3.5, snakemake, and pnnl-atlas are required to be installed prior to execution.

For more information related to bioconda, see:

For more information about Snakemake, see:

Execution Paradigm

The Snakemake environment will be created each time the output directory is altered. For a given experiment, all samples should be defined in a single configuration file, so only one environment needs to be created per experiment.