I’m quite new to galaxy. Recently I’ve been granted access to some dbgap data. I clicked on run selector from dbgap and selected all the files I want to analyse through galaxy. Galaxy gets a list of SRR runs from the dataset fine but when I try to run fasterq-dump to get the fastq files into galaxy, I get the following error:
Downloading accession: SRR4785418…
2023-05-15T11:48:37 fasterq-dump.3.0.3 err: query unauthorized while resolving query within virtual file system module - failed to resolve accession ‘SRR4785418’ - Access denied - please request permission to access phs000472 / DS-CA in dbGaP. ( 403 )
Query SRR4785418: Error 403 Access denied - please request permission to access phs000472 / DS-CA in dbGaP.
I do have access to this. If I were to run fastq-dump on my local machine, I’d need to specify a jwt cart file but I can’t see the option in galaxy. Is it possible to manipulate dbgap controlled access data on galaxy and if so, how?
It sounds like you are currently working at a public Galaxy server, UseGalaxy.org. That server and other public resources, Galaxy or otherwise, are usually not appropriate for privacy-restricted data with secure use requirements.
The good news is that these public servers are just one way to use Galaxy. How others approach working with restricted data is to set up one of the private Galaxy server choices.
Scroll down a bit to the matrix Which Platform / Platform Type to Choose?
Review the recommend choices that fit your use case
Each is described in more detail in the directory above
Platform directory entries will generally include contact information, along with link outs to support and/or configuration resources. Galaxy itself is always free. Compute resources and administration/hosting costs can vary depending on needs.
That is all a bit vague but each choice has complex considerations. Should you have questions about a particular platform, please share back the link to the directory entry, describe your concern, and we can try to help more.