The Illumina DNA sequence for single sample we got was 59 (uncompressed), but I learned that the maximum file you can upload by using FTP should be <50G. Is there any other way I can upload the file to Galaxy?
Split the fasta file locally, then upload the sub-files. Merge once in a history using the tool Concatenate.
Ensure that fasta data is split logically if you wish to use these sub-files independently (meaning that individual fastq records, four lines each, are each fully intact). But, if the data will only be used in the post-Concatenate-merged format with tools, split fastq entries should not trigger problems as these are disposable intermediate datasets.