1 analyses.mk: analysis_to_run
2 echo 'ANALYSES='$$(echo 'load("analysis_to_run"); print(names(analysis.to.run),width=5)'|\
3 $(R) $(ROPTS)|grep -v '^>'|\
4 perl -n -e 'print map {s{\.}{_}g; qq{$$_\n}} m{"([^\"]+)"}g;') > analyses.mk
6 sample_information.txt: sample_information.org
7 grep -v -e '---' -e '^$$' $< |perl -pe 's/^\|\s*|\s*\|$$//g; s/\ *\|\ */\t/g;' > $@;
9 sample_information.xls: sample_information.txt
12 compare_analysis.txt: compare_analysis.R significant_cut combine_analysis
15 significant_cut_summary.txt: array_to_text.R significant_cut
16 $(R) $(ROPTS) -f $< --args significant_cut significant.cuts.summary.table $@
18 significant_cut.txt: array_to_text.R significant_cut annotation_comp
19 $(R) $(ROPTS) -f $< --args significant_cut combined.analysis.cut.array $@
21 significant_cut_plot.pdf: significant_cut_plot.R significant_cut
23 ps2pdf $(patsubst %.pdf,%.ps,$@) $@
24 rm -f $(patsubst %.pdf,%.ps,$@)
26 significant_cut_simplified.txt: array_to_text.R significant_cut_simplified
27 $(R) $(ROPTS) -f $< --args significant_cut_simplified significant.cuts.simplified $@
29 significant_cut_simplified: simplify_significant_cut.R significant_cut
32 significant_cut: significant_cut.R combine_analysis
35 combine_analysis.txt: array_to_text.R combine_analysis
36 $(R) $(ROPTS) -f $< --args combine_analysis combined.analysis.array $@
38 combine_analysis: combine_analysis.R $(patsubst %,%_analysis,$(ANALYSES)) annotation_comp
39 $(R) $(ROPTS) -f $< --args $(patsubst %,%_analysis,$(ANALYSES))
41 %_analysis_plot.pdf: %_analysis plot_analysis.R
42 $(R) $(ROPTS) -f $(filter %plot_analysis.R,$^) --args $< $@
44 %_analysis.txt: %_analysis array_to_text.R
45 $(R) $(ROPTS) -f $(filter %array_to_text.R,$^) --args $< $(subst _,.,$(patsubst %_analysis.txt,%,$@)) $@
47 %_analysis: run_analysis.R sample_information analysis_to_run sample_expression_mas5
48 $(R) $(ROPTS) -f $< --args $(wordlist 2,$(words $^),$^) $@
50 analysis_to_run: analysis_to_run.R sample_grouping
51 $(R) $(ROPTS) -f $< --args $(wordlist 2,$(words $^),$^) $@
53 sample_grouping: sample_grouping.R sample_information
54 $(R) $(ROPTS) -f $< --args $(wordlist 2,$(words $^),$^) $@
56 sample_expression_mas5: make_mas5_expression.R sample_information
57 $(R) $(ROPTS) -f $< --args $(wordlist 2,$(words $^),$^) $@
59 sample_expression_mas5_normalized: make_normalized_expression.R sample_expression_mas5 sample_information
62 sample_expression_mas5_normalized_annotated: make_normalized_annotated.R annotation_comp sample_expression_mas5_normalized
65 sample_expression_mas5_normalized_annotated.txt: array_to_text.R sample_expression_mas5_normalized_annotated
66 $(R) $(ROPTS) -f $< --args sample_expression_mas5_normalized_annotated sample.expression.mas5.normalized.annotated $@
69 sample_expression_mva_plots.pdf: sample_expression_mva_plots.R sample_information sample_expression_mas5 sample_expression_mas5_normalized
72 annotation_comp: make_annotation.R
75 sample_information: make_sample_information.R sample_information.txt
76 $(R) $(ROPTS) -f $< --args $(wordlist 2,$(words $^),$^) $@