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Requirements

1. Required Applications

Install Python 3+
Install GDC Data Transfer Tool Client

Get app to download GDC data, download the GDC Data Transfer Tool Client for your system at the above link. Below is an example for Ubuntu.
```
curl -O https://gdc.cancer.gov/files/public/file/gdc-client_v1.6.1_Ubuntu_x64.zip
unzip gdc-client_v1.6.1_Ubuntu_x64.zip
```

2. Create an environment and install dependencies

python3 -m venv venv; source venv/bin/activate

pip install -r requirements.txt: pip install -r gdan-tmp-models/requirements.txt

3. GDC Client Token

Token setup. Go to https://portal.awg.gdc.cancer.gov/ get token under profile and save as secrets/gdc-awg.token

4. Fetch Classifier Submodule

Intialize and fetch the submodule gdan-tmp-models.

 git submodule init; git submodule update

Make sure to complete each step on the submodule requirements page

And download required data for submodule under Download Required Data

5. Download Required Data

Download these files from the publication page and place in:

src/gdc_download_ref.tar.gz then cd src; tar -xf gdc_download_ref.tar.gz
src/distance_metric/HCMI_AWG_Model-Tumor-Normal_Linkage_v2.0_2.20.2024.txt
src/processed.tar.gz then cd src; tar -xf processed.tar.gz