It might be worthwhile adding BIOY_THREADS (to provide a default) as well as BIOY_BLAST_THREADS and BIOY_SSEARCH_THREADS (for example) to use in place of the corresponding command line flags. If a bit of an edge case that we want to change the number of threads between runs of a single scons pipeline, but it does happen, and it's pretty annoying when otherwise completed steps are forced to re-run when nthreads changes.
It might be worthwhile adding BIOY_THREADS (to provide a default) as well as BIOY_BLAST_THREADS and BIOY_SSEARCH_THREADS (for example) to use in place of the corresponding command line flags. If a bit of an edge case that we want to change the number of threads between runs of a single scons pipeline, but it does happen, and it's pretty annoying when otherwise completed steps are forced to re-run when nthreads changes.