entrez direct private data access

Question

[Synanth]

Hi, I'm trying to use the entrez cli utilities access and download run data from a pre-print. I have the GSE accession number and the access token-- but can't seem to find how to handle the query to be able to download the data in fastq. Any help would be greatly appreciated. Best, Synanth

[GenoMax]

I don't think you can use EntrezDirect to download sequence data or are you referring to something else?

[Synanth]

I should clarify: I want to use EntrezDirect to get and parse SRX numbers which I can then use with fastq-dump. I just don't know how to use the token in the parameters to gain access.

[GenoMax]

Neither esearch or efetch (which is what you would typically use) seem to have command line options to include a token on the command line. Perhaps you need to set a system variable with the token like one does with NCBI_API_KEY?

[Synanth]

Thanks, I'll look into it more and just download the tar via the browser and use scp to transfer it to the workhorse for now.