Thanks for the quick reply.
I've already checked how to configure our Galaxy instance for FTP upload,
but due to security reasons, I cannot use that option. I read the wiki for
Data Libraries and found that uploading via filesystem path can be used
for putting files with size greater than 2GB in Galaxy. Since the data is
stored in the same place where our Galaxy is installed, choosing the link
option in Upload via Filesystem path seemed good enough. Anyway, at least
now I'm sure that Galaxy indeed accepts compressed files.
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