Added dependencies on spell-* binaries.

doc/user_manual/makefile

@@ -48,16 +48,16 @@ input_files/example1_F2.phen: $(EXAMPLE_DIR)/example1_F2.phen
 .inputs: input_files/example1.map input_files/example1_F2.phen input_files/example1_F2.gen input_files/example1.ped
 	touch $@
 
-my_directory/my_name.cache/my_name.spell-pedigree.data: $(EXAMPLE_DIR)/example1.ped
+my_directory/my_name.cache/my_name.spell-pedigree.data: $(EXAMPLE_DIR)/example1.ped $(BINDIR)/spell-pedigree
 	$(BINDIR)/spell-pedigree -wd my_directory -n my_name -p $<
 	
-my_directory/my_name.cache/my_name.spell-marker.data: my_directory/my_name.cache/my_name.spell-pedigree.data $(EXAMPLE_DIR)/example1_F2.gen $(EXAMPLE_DIR)/example1_F2C.gen
+my_directory/my_name.cache/my_name.spell-marker.data: my_directory/my_name.cache/my_name.spell-pedigree.data $(EXAMPLE_DIR)/example1_F2.gen $(EXAMPLE_DIR)/example1_F2C.gen  $(BINDIR)/spell-marker
 	$(BINDIR)/spell-marker -wd my_directory -n my_name -m F2:A/B $(EXAMPLE_DIR)/example1_F2.gen -m F2C:A/C $(EXAMPLE_DIR)/example1_F2C.gen -o F2,F2C -O1 -Op
 
-my_directory/my_name.n-point/ch1/F2/my_name.ch1.F2.0.csv:  my_directory/my_name.cache/my_name.spell-marker.data $(EXAMPLE_DIR)/example1_F2.phen $(EXAMPLE_DIR)/example1_F2C.phen $(EXAMPLE_DIR)/example1.map
+my_directory/my_name.n-point/ch1/F2/my_name.ch1.F2.0.csv:  my_directory/my_name.cache/my_name.spell-marker.data $(EXAMPLE_DIR)/example1_F2.phen $(EXAMPLE_DIR)/example1_F2C.phen $(EXAMPLE_DIR)/example1.map $(BINDIR)/spell-qtl
 	$(BINDIR)/spell-qtl -wd my_directory -n my_name -P auto -p F2 $(EXAMPLE_DIR)/example1_F2.phen -p F2C $(EXAMPLE_DIR)/example1_F2C.phen -gm $(EXAMPLE_DIR)/example1.map output-nppop
 
-my_directory/my_name.report/t1/t1_report.txt: my_directory/my_name.cache/my_name.spell-marker.data $(EXAMPLE_DIR)/example1_F2.phen $(EXAMPLE_DIR)/example1_F2C.phen $(EXAMPLE_DIR)/example1.map
+my_directory/my_name.report/t1/t1_report.txt: my_directory/my_name.cache/my_name.spell-marker.data $(EXAMPLE_DIR)/example1_F2.phen $(EXAMPLE_DIR)/example1_F2C.phen $(EXAMPLE_DIR)/example1.map $(BINDIR)/spell-qtl
 	$(BINDIR)/spell-qtl -wd my_directory -n my_name -P auto -p F2 $(EXAMPLE_DIR)/example1_F2.phen -p F2C $(EXAMPLE_DIR)/example1_F2C.phen -gm $(EXAMPLE_DIR)/example1.map QTL-detection CIM-
 
 output_files/my_name.ch1.F2.0.csv: my_directory/my_name.n-point/ch1/F2/my_name.ch1.F2.0.csv