Question: ICGC data download
0
gravatar for banerjeeshayantan
21 months ago by
banerjeeshayantan110 wrote:

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!

next-gen • 1.1k views
ADD COMMENTlink written 21 months ago by banerjeeshayantan110

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

ADD REPLYlink modified 21 months ago • written 21 months ago by Kevin Blighe43k

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
ADD REPLYlink modified 20 months ago by genomax68k • written 20 months ago by banerjeeshayantan110

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

ADD REPLYlink written 20 months ago by Kevin Blighe43k
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