[galaxy-dev] Freebayes

I'm trying to run Freebayes SNP calling on a bam file from a BWA alignment of solid data. I keep getting the following error:

[bam_sort_core] merging from 40 files... freebayes: invalid option -- Y did you mean --bam ?

I'm not sure where this is set in the code to try to debug things. I'm wondering if anyones had this error, and how to fix it? Just to note, I'm running Brad Chapmans branch of galaxy for the LIMS functionality. But it appears to be an issue with either galaxy-dist or this one.

Thanks in advance for any advice.

Juan Perin