I want to make a pipeline that grabs a reference genome, indexes it, then aligns reads to it via bwa. The bwa tool has a menu option for using an index "from the history" (see attached image) but I don't see any option within the bwa wrappers to actually create an index on the fly. This is also true for samtools and other aligners. The following link describes the conf/loc files required to add indexes to the system: http://wiki.galaxyproject.org/Admin/NGS%20Local%20Setup But how can they be created dynamically in the course of a pipeline run instead of preconfigured in this way? Regards - Joshua