[galaxy-dev] Slow FASTQ-Groomer / Illumina input for tools

Hello, We've processing several FASTQ files (Illumina, of course ;) ), and the FASTQ-Groomer is running for 2.5 hours now. The input files are ~4.5GB / 36nt . First, Is any one else getting faster results ? maybe we're doing something wrong that can be improved. Second, Is any one on the mailing-list have Illumina-capable versions of TopHat/Cufflinks, ones that don't require grooming ? Thanks, -gordon