[galaxy-dev] hg19 reference gnome for Tophat2

I downloaded the entire directory of UCSC for the reference gnome of Tophat2. It turns out that the Tophat2 and Bowtie2 uses the same reference gnome. I found a directory: Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index with the files: genome.1.bt2 genome.2.bt2 genome.3.bt2 genome.4.bt2 genome.rev.1.bt2 genome.rev.2.bt2 While adding the reference gnome, I need to edit bowtie2_indices.loc Shall I replace: /orig/path/hg19 hg19 hg19 /depot/data2/galaxy/bowtie2/hg19/hg19 with hg19 hg19 hg19 Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index Thanks, Sachit