search

abdohlman / tcma_code

Software used to develop the TCMA database associated with 10.1016/j.chom.2020.12.001.
https://tcma.pratt.duke.edu/
12 stars 7 forks source link

token_file for controlled data #1

Closed WeijiaSu closed 1 year ago

WeijiaSu commented 1 year ago

Hello,

I am trying to reproduce the code to download some TCGA raw reads data and/or bam files. I see there a parameter called $token_file, I was wondering how to get this tocken_file to get the access to the controlled data?

Thanks for your help. Weijia

abdohlman commented 1 year ago

Hello! To get a token file you need to apply for access through dbGap. Once you've done so, you'll log in to your NIH account from the GDC portal. Then click your username on the top ribbon and select "Download Token" from the dropdown menu.