Batch Glimmer3 annotation for multiple fastas

Question

[oliver.bayfield]

I have a fasta nt file containing about 2000 bacterial/archeal entries, and I'd like to use something like glimmer to do the gene calling inside each fasta sequence, each of about 3000nt (I predict 2 or 3 genes each entry).
Is there a server that would allow a batch upload and then treat each entry separately? Output could be in genbank format or protein fasta.
I know RAST has something like this but with the way I've submitted it I think it's going to try to assemble all my ~2000 "contigs" - correct me if I'm wrong - which isn't desirable.

[h.mon]

Maybe MG-RAST?