Hi guys, I'm getting this error when running tophat for Illumina: Error in tophat: [2013-02-20 16:43:50] Beginning TopHat run (v2.0.6) ----------------------------------------------- [2013-02-20 16:43:50] Checking for Bowtie Bowtie version: 2.0.2.0 [2013-02-20 16:43:50] Checking for Samtools [2013-02-20 16:43:50] samtools_path: None [2013-02-20 16:43:50] samtools_path after prog_path: /usr/local/galaxy/installs/bin/samtools-0.1.18/samtools Samtools version: 0.1.18.0 [2013-02-20 16:43:50] Checking for Bowtie index files Error: Could not find Bowtie 2 index files (/usr/local/galaxy/indexes/Mus_musculus/UCSC/mm10/Sequence/BowtieIndex.*.bt2) But this is what's in my galaxy-dist/tool-data/bowtie2_indices.loc file: mm10 mm10 mm10 /usr/local/galaxy/indexes/Mus_musculus/UCSC/mm10/Sequence/Bowtie2Index Why isn't it looking in that directory for the bowtie2 files? It's almost as if it's reading my bowtie_indices.loc file instead? Thanks, Greg