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
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