--- a/Makefile
+++ b/Makefile
@@ -183,7 +168,7 @@
 
 $(BIN_DIR)/intersectBed: | $(BIN_DIR)
 	@echo "- Creating executables for old CLI."
-	@python scripts/makeBashScripts.py
+	$(EPYTHON) scripts/makeBashScripts.py
 	@chmod +x bin/*
 	@echo "done."
 
--- a/src/utils/BamTools/Makefile.frag
+++ b/src/utils/BamTools/Makefile.frag
@@ -1,4 +1,4 @@
 src/utils/BamTools/include/BamAlignment.mapping.hpp: src/utils/BamTools/mapping/BamAlignment.py src/utils/BamTools/mapping/BamAlignment.map
 
 src/utils/BamTools/include/%.mapping.hpp: src/utils/BamTools/mapping/%.py src/utils/BamTools/mapping/%.map
-	python $^ > $@
+	$(EPYTHON) $^ > $@
--- a/test/bigchroms/test-bigchroms.sh
+++ b/test/bigchroms/test-bigchroms.sh
@@ -28,7 +28,7 @@
 rm obs
 
 if [[ "$BT_NO_BIG_FILES" != "" ]]; then
-python make-big-chrom.py
+${EPYTHON} make-big-chrom.py
 
 echo -e "    bigchroms.t03...big get fasta \c"
 $BT getfasta -fi bigx.fasta -bed bigx.bed | tail -1 > obs
--- a/test/fisher/cmp.sh
+++ b/test/fisher/cmp.sh
@@ -3,7 +3,7 @@
 echo "fisher,shuffled"
 
 for i in $(seq 1000); do
-    fisher=$(python ./sim.py | tail -1 | cut -f 2)
+    fisher=$(${EPYTHON} ./sim.py | tail -1 | cut -f 2)
     shuffle=$(bash shuf.sh)
     echo "$fisher,$shuffle"
 done