Work around GNU Make's whims.

doc/user_manual/makefile

@@ -6,7 +6,7 @@ EXAMPLE_DIR = $(SRCDIR)/examples/three_parents_F2
 
 all: user_manual.pdf
 
-user_manual.pdf: spell-pedigree.tex spell-marker.tex spell-qtl.tex spell-qtl-examples.tex version.tex user_manual.tex images/Spell-pipeline2.svg inputs outputs
+user_manual.pdf: spell-pedigree.tex spell-marker.tex spell-qtl.tex spell-qtl-examples.tex version.tex user_manual.tex images/Spell-pipeline2.svg .inputs .outputs
 	pdflatex --shell-escape user_manual.tex && pdflatex --shell-escape user_manual.tex > /dev/null
 
 version.tex: 
@@ -36,8 +36,8 @@ input_files/example1.map input_files/example1_F2.phen input_files/example1_F2.ge
 	mkdir -p input_files
 	awk -v len=69 '{ if (length($$0) > len) print substr($$0, 1, len-3) "..."; else print; }' $< > $@
 
-inputs: input_files/example1.map input_files/example1_F2.phen input_files/example1_F2.gen input_files/example1.ped
-
+.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
 	$(BINDIR)/spell-pedigree -wd my_directory -n my_name -p $<
@@ -51,7 +51,8 @@ my_directory/my_name.n-point/ch1/F2/my_name.ch1.F2.0.csv:  my_directory/my_name.
 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 -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
 	
-outputs: my_directory/my_name.report/t1/t1_report.txt my_directory/my_name.n-point/ch1/F2/my_name.ch1.F2.0.csv
+.outputs: my_directory/my_name.report/t1/t1_report.txt my_directory/my_name.n-point/ch1/F2/my_name.ch1.F2.0.csv
+	touch $@
 
 clean:
 	rm -f *.aux *.log *.pdf *.toc *.out *.lol