Remove unused file

Makefile

-#!/usr/bin/make -f
-# Makefile for running the INF pipeline
-# Author: Marco Chierici <chierici@fbk.eu>
-# Date: 2017-05-12
-#
-.PHONY: init
-
-SHELL := /bin/bash
-
-# input variables
-# shown are examples, override on command line
-FILE ?= data/AG1-G_MAV-G_498_LIT_ALL_tr.txt
-LABEL ?= data/label_498_ALL-EFS_tr.lab
-DATA1 ?= data/AG1-G_498_LIT_ALL_tr.txt
-DATA2 ?= data/MAV-G_498_LIT_ALL_tr.txt
-ENDPOINT ?= ALL-EFS
-# added MF 20170710
-THREADS ?= 4
-OUTBASE ?= /path/to/out_tmp
-
-BINDIR := .
-OUTDIR := $(OUTBASE)/$(ENDPOINT)
-
-# derived variables
-OUTPREFIX = $(notdir $(basename $(FILE)))
-LEVEL1 = $(word 1,$(subst _, ,$(OUTPREFIX)))
-LEVEL2 = $(word 2,$(subst _, ,$(OUTPREFIX)))
-
-init:
-	@mkdir -p $(OUTDIR)/rSNFi
-	@mkdir -p $(OUTDIR)/rSNF
-
-all: init $(OUTDIR)/rSNFi/$(OUTPREFIX)_MCC_scores.txt $(OUTDIR)/rSNF/$(OUTPREFIX)_MCC_scores.txt $(OUTDIR)/juxt/$(OUTPREFIX)_MCC_scores.txt
-
-
-$(OUTDIR)/juxt/$(OUTPREFIX)_RandomForest_KBest.log: $(FILE) $(LABEL)
-	python $(BINDIR)/sklearn_rf_training_fixrank.py $(word 1,$^) $(word 2,$^) $(OUTDIR)/juxt --ranking KBest
-
-
-$(OUTDIR)/juxt/$(OUTPREFIX)_MCC_scores.txt: $(OUTDIR)/juxt/$(OUTPREFIX)_RandomForest_KBest.log $(subst _tr,_ts,$(FILE)) $(subst _tr,_ts,$(LABEL))
-	python $(BINDIR)/sklearn_rf_validation_writeperf.py $(word 1,$^) $(word 2,$^) $(OUTDIR)/juxt --tslab $(word 3,$^)
-
-
-$(OUTDIR)/rSNF/INF_$(OUTPREFIX).txt: $(DATA1) $(DATA2) $(LABEL)
-	Rscript $(BINDIR)/snf_integration.R --d1 $(word 1,$^) --d2 $(word 2,$^) --lab $(word 3,$^) \
-		--scriptDir $(BINDIR)/SNFtools/ --clust spectral --threads "$(THREADS)" \
-		--outf $@
-
-
-$(OUTDIR)/rSNF/$(OUTPREFIX)_RandomForest_rankList.log: $(FILE) $(LABEL) $(OUTDIR)/rSNF/INF_$(OUTPREFIX).txt
-	python $(BINDIR)/sklearn_rf_training_fixrank.py $(word 1,$^) $(word 2,$^) $(OUTDIR)/rSNF \
-		--ranking rankList --rankFeats $(word 3,$^)
-
-
-$(OUTDIR)/rSNF/$(OUTPREFIX)_MCC_scores.txt: $(OUTDIR)/rSNF/$(OUTPREFIX)_RandomForest_rankList.log $(subst _tr,_ts,$(FILE)) $(subst _tr,_ts,$(LABEL))
-	python $(BINDIR)/sklearn_rf_validation_writeperf.py $(word 1,$^) $(word 2,$^) $(OUTDIR)/rSNF --tslab $(word 3,$^)
-
-
-$(OUTDIR)/rSNFi/intersection_$(OUTPREFIX).txt: $(OUTDIR)/juxt/$(OUTPREFIX)_RandomForest_KBest.log $(OUTDIR)/rSNF/$(OUTPREFIX)_RandomForest_rankList.log
-	python $(BINDIR)/intersect_biomarkers.py $(word 1,$^) $(word 2,$^) $(OUTDIR)/rSNFi/venn_$(OUTPREFIX).png $@ --title1 "$(LEVEL1)" --title2 "$(LEVEL2)"
-
-
-$(OUTDIR)/rSNFi/$(OUTPREFIX).txt: $(FILE) $(OUTDIR)/rSNFi/intersection_$(OUTPREFIX).txt
-	python $(BINDIR)/extract_topfeats_onecol.py $(word 1,$^) $(word 2,$^) $@
-
-
-$(OUTDIR)/rSNFi/$(OUTPREFIX)_RandomForest_KBest.log: $(OUTDIR)/rSNFi/$(OUTPREFIX).txt $(LABEL)
-	python $(BINDIR)/sklearn_rf_training_fixrank.py $(word 1,$^) $(word 2,$^) $(OUTDIR)/rSNFi --ranking KBest
-
-
-$(OUTDIR)/rSNFi/$(OUTPREFIX)_MCC_scores.txt: $(OUTDIR)/rSNFi/$(OUTPREFIX)_RandomForest_KBest.log $(subst _tr,_ts,$(FILE)) $(subst _tr,_ts,$(LABEL))
-	python $(BINDIR)/sklearn_rf_validation_writeperf.py $(word 1,$^) $(word 2,$^) $(OUTDIR)/rSNFi --tslab $(word 3,$^)
-