All dependencies are installed via conda using the bioconda channel. The workflow and some dependencies require Python 3.5.
The intended usage requires conda.
With conda, execute:
conda install -c bioconda python=3.5 snakemake bbmap=37.17 click
Using Python 3.5, install atlas:
pip install -U pnnl-atlas
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/
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 30 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.
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