Makefile

TCGA_SCORES = $(shell find ../../scores/tcga -name "*.RData")

CONT_ASSOCS = $(TCGA_SCORES:../../scores/tcga/pathways_%.RData=assocs_cont_%.RData)
DISCR_ASSOCS = $(TCGA_SCORES:../../scores/tcga/pathways_%.RData=assocs_discr_%.RData)

CONT_PLOTS = $(CONT_ASSOCS:assocs_%.RData=plot_%.pdf)
DISCR_PLOTS = $(DISCR_ASSOCS:assocs_%.RData=plot_%.pdf) plot_discr_all/mutation.RData

include ../../Makefile.inc
#$(call ext_dep,../../scores/tcga,$(notdir $(CONT) $(DISCR)))

MAPPED = $(call contains,_mapped,$(DISCR_PLOTS) $(CONT_PLOTS))


all: $(CONT_PLOTS) $(DISCR_PLOTS)

mapped: $(call contains,_mapped,$(DISCR_PLOTS) $(CONT_PLOTS))


$(CONT_ASSOCS): assocs_cont_%.RData: assocs_cont.r util.r ../../scores/tcga/pathways_%.RData
	@mkdir -p $(dir $@)
	$(call bsub_log,4096) Rscript $< $(word 3,$^) $@

$(DISCR_ASSOCS): assocs_discr_%.RData: assocs_discr.r util.r ../../scores/tcga/pathways_%.RData
	@mkdir -p $(dir $@)
	$(call bsub_log,4096) Rscript $< $(word 3,$^) $@

assocs_discr_all/mutation.RData: assocs_mut.r util.r ../tcga_pathway_per_mutation/mut_driver_matrix.RData
	@mkdir -p $(dir $@)
	$(call bsub_log,4096) Rscript $< $(word 3,$^) $@
	

plot_discr_all/mutation.pdf: plot.r assocs_discr_all/mutation.RData
	@mkdir -p $(dir $@)
	Rscript $^ $@

$(CONT_PLOTS) $(DISCR_PLOTS): plot_%.pdf: plot.r assocs_%.RData
	@mkdir -p $(dir $@)
	Rscript $^ $@

bootstrap_highlight.RData: bootstrap_highlight.r ../../scores/tcga/pathways_mapped/speed_matrix.RData
	Rscript $^ $@