How can I import TARGET data into RStudio?

Post author
Sehyun Oh

Hi! I saw a similar post with my question (https://support.terra.bio/hc/en-us/community/posts/360073223011-How-can-I-get-TCGA-data-into-the-notebooks-for-analysis-? ), but it doesn't fully solve my issue. 

1. I need to make my own 'copy' of the Terra-hosted dataset to my bucket to access it? I just want to make sure that I understand this point correctly.

2. I ran this workflow (https://anvil.terra.bio/#workspaces/broad-firecloud-tcga/TARGET_AML_hg38_OpenAccess_GDCDR-12-0_DATA/workflows/broadinstitute_cga/gdc_file_downloader__RNAseq__HTSeqCounts__gene_expression_quantification__txt__cfg) to export the RNAseq count matrix of TARGET_AML dataset, but it failed. It's somewhat cumbersome to find the error message, which is still not informative enough to resolve my issue. Here is the stderr:

Traceback (most recent call last):
  File "/opt/src/disk_size_calculator.py", line 71, in <module>
    main()
  File "/opt/src/disk_size_calculator.py", line 51, in main
    file_metadata=file_metadata_retriever.get_metadata(file_uuid)
  File "/opt/src/disk_size_calculator.py", line 26, in get_metadata
    return responseDict['data']
KeyError: 'data'

Could you help me to resolve this issue? Thanks!

- Sehyun

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