- Leave all settings as default to use test dataset on SKCM tumor samples.
- Download Firehose data for tumor type of interest:
- Set cancer_type to tumor type abbreviation (see: https://gdac.broadinstitute.org/)
- Set date_data to '2016_01_28' to download the latest dataset or an older dataset (see: http://gdac.broadinstitute.org/runs/info/analyses__runs_list.html)
- Set date_data to "2016_07_15" to download the latest dataset or specify another date to use an older dataset (see: http://gdac.broadinstitute.org/runs/info/analyses__runs_list.html)
- Use your own dataset as input by specifying "input_file".
6. The settings for running GISTIC2.0 and for benchmarking can be modified if necessary (see Settings for more information).
7. Run the pipeline shell script, which will create the required conda environment and run snakemake (recommended when snakemake is not installed yet):
```
bash run_pipeline.sh
bash run_pipeline_cluster.sh
```
Or manually install the required packages and run snakemake (recommended when snakemake is already installed):
