Makefile

.PHONY: clean test

clean:
		rm -rf 3d_monolayer/output
		rm -rf AdvancedSegmentation/output
		rm -rf QualityControl/output
		rm -rf PixelBasedClassification/output
		rm -rf Translocation/output

test:
		cellprofiler -c -r -p 3d_monolayer/3d_monolayer_final.cppipe \
		    -i 3d_monolayer/images                                   \
		    -o 3d_monolayer/output                                   \
		    -d 3d_monolayer/output/done

		cellprofiler -c -r -p AdvancedSegmentation/BBBC022_Analysis_Final.cppipe \
		    -i internal_use/runtime_images/BBBC022images                                       \
		    -o AdvancedSegmentation/output                                       \
		    -d AdvancedSegmentation/output/done

		cellprofiler -c -r -p QualityControl/BBBC022_QC.cppipe \
		    -i internal_use/runtime_images/BBBC022images                                       \
		    -o QualityControl/output                                       \
		    -d QualityControl/output/done

		cellprofiler -c -r -p PixelBasedClassification/pixel_based_classification_cho.cppipe \
		    -i PixelBasedClassification/images                                       \
		    -o PixelBasedClassification/output                                       \
		    -d PixelBasedClassification/output/done

		cellprofiler -c -r -p Translocation/Translocation_final.cppipe \
		    -i Translocation/TranslocationData                                    \
		    -o Translocation/output                                    \
		    -d Translocation/output/done

		@if [ $$(cat 3d_monolayer/output/done) = Failure ] ||         \
		    [ $$(cat AdvancedSegmentation/output/done) = Failure ] || \
		    [ $$(cat QualityControl/output/done) = Failure ] || \
		    [ $$(cat PixelBasedClassification/output/done) = Failure ] || \
		    [ $$(cat Translocation/output/done) = Failure ]; then     \
		    false;                                                    \
		else true; fi