Frequently I have a problem like this...
%.error.summary : data/references/HMP_MOCK.fasta %.fasta %.names
$(eval FASTA=$(subst error.summary,fasta,$@)) \
$(eval NAMES=$(subst error.summary,names,$@)) \
mothur "#seq.error(fasta=$(FASTA), name=$(NAMES), reference=data/references/HMP_MOCK.fasta, aligned=F, processors=12)"
What I'd like to be able to do is something like this...