- Set workdir to the directory where the output should be saved.
- Set gisticdir to the directory where GISTIC2 should be installed or where GISTIC2 has already been installed.
- There are three options for input data:
- 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)
- Use your own dataset as input by specifying "input_file".
- The settings for running GISTIC2.0 and for benchmarking can be modified if necessary.
6. Run the pipeline shell script, which will create the required conda environment and run snakemake (recommended when snakemake is not installed yet):
