If you have a git clone of cBioPortal, the relevant scripts can be found in the folder: <your_cbioportal_dir>/core/src/main/scripts/importer
The scripts run in Python 3.4 or newer, and they require the modules requests and pyyaml. You can use this command to install those modules:
$ sudo python3 -m pip install requests pyyaml
If you want the scripts to be able to generate html reports (recommended way for reading the validation errors, if any), then you will also need to install Jinja2. You can use this command:
$ sudo python3 -m pip install Jinja2
Preparing Study Data
A study to be loaded in cBioPortal can basically consist of a directory where all the data files are located. Each data file needs a meta file that refers to it and both files need to comply to the format required for the specific data type. The format and fields expected for each file are documented in the File Formats page. Below is an example of the files in such a directory.
Examples for the different types of data are available on the File Formats page. The Provisional TCGA studies, downloadable from the Data Sets section are complete studies that can be used as reference when creating data files.