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:


But how can they be created dynamically in the course of a pipeline run
instead of preconfigured in this way?

Regards -


<<attachment: galaxy_bwa_index_input.jpg>>

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