Hi, I'm trying to get Bismark running on my Galaxy instance, but am having problems which I think are related to the location of the indices. For various permissions reasons, I can't put the Bismark indices in the normal Galaxy Bowtie directory, so instead I've created the tool-data/bowtie_indices.loc file within the Bismark tool directory specifying a different location for these files. But when I run Bismark (from within Galaxy) I get an empty output file with a message in the history entry listing the reference genome directory as the default Galaxy one, not the one specified in the Bismark bowtie_indices.loc (full output given below - the apparent truncation at the end is as it is shown in the history).
The history entry is green, suggesting that whatever has gone wrong, the tool wrapper has returned a success value back to Galaxy. Also the program works fine from the command line. Any suggestions please? Thanks very much.
Error in bismark: Path to Bowtie specified as: bowtie Alignments will be written out in BAM format. Samtools found here: '/usr/local/bin/samtools' Reference genome folder provided is /mnt/galaxyIndices/genomes/hg19/bowtie_index/ (absolute path is '/mnt/g