from galaxy to ncbi GEO

I’ve in my galaxy account a collection of fastq files that i would like to upload to the ncbi GEO upload service prior to publication. I guess most are already familiar with this type of uploads, but anyway, it’s an ftp server with an username and password (details here https://www.ncbi.nlm.nih.gov/geo/info/submissionftp.html but you need to be logged into NCBI to see this, because details are different for each user).

It is there any way to do this directly, without transferring the files from my computer? I found some cloud export options but, surprisingly, not NCBIs GEO…

please note that this is not the question frequently asked about from to download GEO files into galaxy but precisely the opposite direction, from galaxy to GEO.

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Hi @r12

Correct, you won’t be able to log into a secure account from a public Galaxy server.

Why? All data connections are technically “public” at these sites (although, not how a person would think of it – is more about how computers work under the hood – your password protected work is not actually public!).

From your computer is likely the choice if I am understanding correctly. Unless they also support secure cloud buckets (you could check with them for which).

The same is true for downloads from secure environments – the public servers will not work for this – but there are private Galaxy server versions that are configured work with specific sites, AnVIL is one example.

Hope that helps!