[galaxy-dev] Default annotation track

I needed to add a genome to the tracks in our local instance. However, the only available genome is a multi-fasta file of about 1800 supercontigs. I preserve the sanity of my clients I concatenated the fasta file and provided both versions. The unfortunate part is that the contig annotation data is lost in that conversion. I wonder if there is a way to extract the contig data as annotation and provide it as a default track in the concatenated genome or something like that. Any ideas? Thanks, Alex