About this repository

This repository is intended to provide you with easy-to-follow instructions to prepare your study data for upload into cBioportal.

The repository is structured into four sections:

1. 01_file_formats: Helpful instructions on how to format clinical and genomic data files for upload to cBioportal. Templates that can be modified for uploading your study.

2. 02_resource: List of resources that are useful when preparing your files for cBioPortal. These are specific to the FH instance

3. 03_launch_local: Instructions on how to launch a local version of cBioportal on your computer and test the upload of your study or the example study. You would want to do this to ensure that your study data files are formatted correctly and appear they way you intend prior to upload into the public-facing cBioportal instance.

4. 04_example_study: An example study (from the Berger Lab at Fred Hutch) that can be either used as a template for your own study or can be used to test the useful_tools or the local instance of cBioportal. This is how your study folder should look like once it is ready for upload into cBioPortal.(Note: You may have more or less files depending on your study)

5. 05_useful_tools: A collection of public repositories and helpful instructions that can help with formatting different types of study data files.

How do I make a copy of this repository on my local computer?

Here are some instructions to get a local copy of this repository. By making a local copy of the repository you can edit the templates etc. locally for your particular use case.

Go to the directory on your computer where you want to clone a repository

cd /path/to/directory/

Clone this repository

git clone https://github.com/FredHutch/tg-cbioportal-data