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Bioconductor / GenomicDataCommons

Provide R access to the NCI Genomic Data Commons portal.
http://bioconductor.github.io/GenomicDataCommons/
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error on download MAF files #56

Closed bioinfo-dirty-jobs closed 6 years ago

bioinfo-dirty-jobs commented 6 years ago

I have this error:


dati3=files() %>% filter(~ cases.case_id %in% tolower(data[,1]) &
                            data_format=="MAF" &
                           analysis.workflow_type=="MuTect2 Variant Aggregation and Masking") %>%   ids()
gdcdata(dati3,progress=TRUE)
GDC Cache directory set to: /home/maurizio/.cache/GenomicDataCommons
  |=============================================================================================================| 100%
Error in (function (uri, destination, overwrite, progress, token = NULL,  : 
  Forbidden (HTTP 403).
seandavi commented 6 years ago

You are trying to download controlled-access data, it appears. You'll either need to apply for access to TCGA data and use an access token or specify that the data are access=="open".

dati3=files() %>% filter(~ cases.case_id %in% tolower(data[,1]) &
                            data_format=="MAF" & 
                            access=="open" &
                           analysis.workflow_type=="MuTect2 Variant Aggregation and Masking") %>%   ids()
gdcdata(dati3,progress=TRUE)