ENH: Run project with single make command (in progress)

Makefile

@@ -0,0 +1,87 @@
+# To run everything:
+#
+#   make
+#
+# For help running specific parts:
+#
+#   make help
+
+# Overwritable paths to executables
+CELLPROFILER := cellprofiler
+PYTHON := python
+RSCRIPT := Rscript
+
+# Make rule sources and targets
+SOURCES_img_raw := data/April_14_2016.tar.xz
+TARGETS_img_raw := data/April_14_2016
+SOURCES_img_zproj := $(TARGETS_img_raw)
+TARGETS_img_zproj := results/z_projection
+SOURCES_img_filelist := $(TARGETS_img_zproj)
+TARGETS_img_filelist := results/cellprofiler/filelist
+SOURCES_cellprofiler_filelist := $(TARGETS_img_filelist)
+SOURCES_cellprofiler_pipe := src/image-processing-pipeline.cpproj
+SOURCES_cellprofiler_img := $(TARGETS_zproj)
+SOURCES_cellprofiler := $(SOURCES_cellprofiler_filelist) \
+	$(SOURCES_cellprofiler_pipe) $(SOURCES_cellprofiler_img)
+TARGETS_cellprofiler_db := results/cellprofiler/all-plates.db
+TARGETS_cellprofiler_prop := results/cellprofiler/all-plates.properties
+TARGETS_cellprofiler := $(TARGETS_cellprofiler_db) $(TARGETS_cellprofiler_prop)
+define CELLPROFILER_OPTS
+--pipeline=$(SOURCES_cellprofiler_pipe) \
+--file-list=$(SOURCES_cellprofiler_filelist) \
+--output-directory=$(dir $(TARGETS_cellprofiler_db))
+endef
+SOURCES_signif_wells := $(TARGETS_cellprofiler_db)
+TARGETS_signif_wells := results/tables/rnai-p_values.csv
+SOURCES_plot_overlap := $(TARGETS_signif_wells)
+TARGETS_plot_overlap := $(addsuffix results/plots/,)
+SOURCES_plot_plates := $(TARGETS_signif_wells)
+TARGETS_plot_plates := $(addsuffix results/plots/,)
+TARGETS_plots := $(TARGETS_plot_overlap) $(TARGETS_plot_plates)
+
+.PHONY : all
+all : z-projection cellprofiler plots ## (Default) Run full pipeline from image processing to plots.
+
+# Self-documenting help modified from
+# https://gist.github.com/prwhite/8168133#gistcomment-1737630
+.PHONY : help
+help : 				## Show this help.
+	@echo -e 'Usage: make [TARGET] ...\n\nTargets:'
+	@sed -nE 's|^(\S+)[^#]+##(.+)|\1\t\2|p'  $(MAKEFILE_LIST) | column -t -s '	'
+
+# More robust would be to associate individual target TIF files
+# contained in the tarball, but reading the archive takes a long time
+# and adds overhead to Makefile processing.
+$(TARGTS_img_raw) : $(SOURCES_img_raw)
+	cd data; tar -xvJpf $<
+
+.PHONY : z-projection
+z-projection : $(TARGETS_img_zproj) ## Generate maximum intensity projection images.
+$(TARGETS_img_zproj) : $(SOURCES_img_zproj)
+	$(PYTHON) src/image_preprocessing_z_projection.py $< $@
+
+.PHONY : cellprofiler
+cellprofiler : $(TARGETS_cellprofiler) ## Collect statistics about all images.
+$(TARGETS_cellprofiler) : $(SOURCES_cellprofiler)
+	$(CELLPROFILER) $(CELLPROFILER_OPTS) --run-headless
+
+.PHONY : gui-cellprofiler
+gui-cellprofiler : $(SOURCES_cellprofiler) ## Interactively run CellProfiler.
+	$(CELLPROFILER) $(CELLPROFILER_OPTS)
+
+$(TARGETS_img_filelist) : $(abspath $(SOURCES_img_filelist))
+	find $< -type f | sort > $@
+
+.PHONY : plots
+plots : $(TARGETS_plots)
+
+$(TARGETS_plot_overlap) : $(SOURCES_plot_overlap)
+	$(RSCRIPT) src/plots.R
+
+$(TARGETS_plot_plates) : $(SOURCES_plot_plates)
+	$(RSCRIPT) src/plot-plates.R
+
+.PHONY : clean-all
+clean-all :			## Delete all output.
+	rm -rf $(TARGETS_img_raw)
+	rm -rf results/*