Create a Python configuration file parsl_config.py
in workspace config
dir using one of the available templates (parsl_config.py.template
)
Create a json configuration file gdc_config.json
in workspace config
dir using the template gdc_config.json.template
-
Download GDC-Pipeline resource files
./scripts/gdc-installer.sh
-
Generate indexes for genome reference
./scripts/gdc-generate-ref-index.sh
-
Install dependencies and setup conda environment
./scripts/gdc-installer.sh
-
Use configuration defined in
gdc_config.json
python run.py
-
Override parameters defined in
gdc_config.json
using environment variablesGDC_BAM_INPUT=<input_campaign.json> GDC_CONFIG_FILE=<gdc_config_env.json> python ./run.py