RapMap: reference transcriptome for simulated reads
Thanks for your interest in RapMap.

At that time we were using flux simulator for simulating read sequence data. We used the genome and gtf file together as an input to flux. 

I dug into the scripts and got hold of the gtf link ftp://ftp.ensembl.org/pub/release-80/gtf/homo_sapiens/Homo_sapiens.GRCh38.80.gtf.gz, 
and the genome file link ftp://ftp.ensembl.org/pub/release-80/fasta/homo_sapiens/dna/Homo_sapiens.GRCh38.dna.toplevel.fa. 

We used rsem-prepare-reference to create the reference transcriptome file later in order to run RapMap and other transcriptome based quantification tools. I hope this helps. 

PS: I am a coauthor of the RapMap paper.