View of /8fly/Makefile

#PFOLDSCAN = $(HOME)/pfold/pfoldscan.pl
PFOLDSCAN = /mnt/nfs/pfold/pfoldscan.pl

# Break up the processing of the alignment files into 10 batches (0-9).

# Get all the files in align subdirectory that end in "0.fa".
# Substitute "scan" for "align" in pathname.
# Substitute ".pfoldscan" for ".fa" in extension.
batch0: $(subst .fa,.pfoldscan,$(subst align,scan,$(wildcard align/*0.fa)))

batch1: $(subst .fa,.pfoldscan,$(subst align,scan,$(wildcard align/*1.fa)))

batch2: $(subst .fa,.pfoldscan,$(subst align,scan,$(wildcard align/*2.fa)))

batch3: $(subst .fa,.pfoldscan,$(subst align,scan,$(wildcard align/*3.fa)))

batch4: $(subst .fa,.pfoldscan,$(subst align,scan,$(wildcard align/*4.fa)))

batch5: $(subst .fa,.pfoldscan,$(subst align,scan,$(wildcard align/*5.fa)))

batch6: $(subst .fa,.pfoldscan,$(subst align,scan,$(wildcard align/*6.fa)))

batch7: $(subst .fa,.pfoldscan,$(subst align,scan,$(wildcard align/*7.fa)))

batch8: $(subst .fa,.pfoldscan,$(subst align,scan,$(wildcard align/*8.fa)))

batch9: $(subst .fa,.pfoldscan,$(subst align,scan,$(wildcard align/*9.fa)))

# "$*" matches the stem "%" of the rule target 
# "$<" matches the name of the rule prerequisite
# "$@" matches the name of the rule target
scan/%.pfoldscan: align/%.fa
	@echo '>>>>> Starting' $@ '>>>>>' `date`
#	$(PFOLDSCAN) -paml -o work/$* $< >$@
	$(PFOLDSCAN) -paml -x -d /mnt/nfs/dart/bin.darwin -p /mnt/nfs/pfold/bin.darwin -pamlDir /mnt/nfs/paml/bin.darwin -o work/$* $< >$@
#	$(PFOLDSCAN) -paml -x -d /mnt/nfs/dart/bin -p /mnt/nfs/pfold/bin -pamlDir /mnt/nfs/paml/bin -o work/$* $< >$@
	@echo '<<<<< Ending' $@ '<<<<<' `date`

clean:
	rm -rf scan work