ICGC data download

Question

[Gene_MMP8]

I am new to the ICGC data verse. I would like to download some bam files specific to my interest in a particular cancer type. I am trying very hard to install all the dependencies like docker etc, before downloading the data, but some error or the other keeps coming up. In addition to that, I am confused with the different types of data, their repositories etc. Can someone point me to a nice tutorial that takes a hands-on approach and teaches how to download data from ICGC? After a frustrating day of trying to figure out, I am posting this. Please help!

[Kevin Blighe]

Are you trying to use the icgc-get program to download the data? What is the error message that you are getting?

[Gene_MMP8]

Hi Kevin, sorry for the late reply. The following is the error when I trying to run the download command

  | nohup: redirecting stderr to stdout
  | Starting...
  | 
  | Running...
  | 
  | Validating repository connection...
  | 
  | ERROR: Command error: java.io.IOException: Access refused by repository. Ensure client is running as part of repository cloud.
  | 
  | Please check the log for detailed error messages
collaboratory client exited with a nonzero error code 1.
Error: Please check client output for error messages

[Kevin Blighe]

Hmm.... I would encourage you to post the issue on the GitHub page: https://github.com/icgc/icgc-get/issues