I got this error which executing tophat2 in Galaxy: Error in tophat: [2013-02-13 02:02:43] Beginning TopHat run (v2.0.7) ----------------------------------------------- [2013-02-13 02:02:43] Checking for Bowtie Bowtie version: 2.0.6.0 [2013-02-13 02:02:43] Checking for Samtools Samtools version: 0.1.18.0 [2013-02-13 02:02:43] Checking for Bowtie index files Error: Could not find Bowtie 2 index files (/data/bowtie2-2.0.6/hg19/Homo_sapiens/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/.*.bt2) The tool produced the following additional output: TopHat v2.0.7 tophat2 -p 4 /data/bowtie2-2.0.6/hg19/Homo_sapiens/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/ /opt/galaxyprod/galaxy-dist/database/files/000/dataset_197.dat I have these files under the Index directory: genome.1.bt2 genome.2.bt2 genome.3.bt2 genome.4.bt2 genome.fa genome.rev.1.bt2 genome.rev.2.bt2 tophat_out