I have a local instance of galaxy running. I'm trying to allign some paired end fastq files to a reference. I've installed bwa through the tool shed but when I try and run it, it returns an error saying
Tool execution generated the following error message:
Error indexing reference sequence. /bin/sh: 1: bwa: not found
The tool produced the following additional output:
Could not determine BWA version
Does anyone know what's going wrong here?