conda install python=3.5 snakemake
The intended usage requires
Using Python 3.5, install
pip install -U pnnl-atlas
atlas should be executable:
$ atlas -h Usage: atlas [OPTIONS] COMMAND [ARGS]... ATLAS Options: --version Show the version and exit. -h, --help Show this message and exit. Commands: assemble assembly workflow download download reference files make-config prepopulate a configuration file with samples and defaults ...
As ATLAS executes rules to generate output files, an environment is created
snakemake --use-conda in the background. No dependencies aside from
python 3.5, snakemake, and pnnl-atlas are required to be installed prior to
For more information related to bioconda, see: https://bioconda.github.io/
For more information about Snakemake, see: https://snakemake.readthedocs.io
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.