67eca6b636d365e436b5aa1bcba7316fd60d27aa
hiram
  Mon Nov 14 22:45:24 2022 -0800
generic makefile to function on linux and in Mac OSX environment refs #29651

diff --git src/utils/findMotif/tests/makefile src/utils/findMotif/tests/makefile
index 1cb6885..ec834e2 100644
--- src/utils/findMotif/tests/makefile
+++ src/utils/findMotif/tests/makefile
@@ -1,66 +1,74 @@
 
+SHELL := /bin/bash
+
+findMotif=findMotif
+# use local binary if available
+ifneq ($(wildcard ../findMotif),)
+  findMotif=../findMotif
+endif
+
 testList = test1 test2 test3 test4 test5 test6 test7 test8 test9 \
 	test10 test11
 
 test: ${testList}
 
 test1:
-	@findMotif -verbose=3 -motif=TACTAAACCC hg19.chrM.fa.gz 2>&1 | grep -v "kent source version" > test1.txt 2>&1
-	@zdiff -q test1.txt expected/test1.txt.gz
+	@${findMotif} -verbose=3 -motif=TACTAAACCC hg19.chrM.fa.gz 2>&1 | grep -v "kent source version" > test1.txt 2>&1
+	@diff -q test1.txt <(gunzip -c expected/test1.txt.gz)
 	@ rm -f test1.txt
 
 test2:
-	@findMotif -verbose=2 -motif=GGGTTTAGTA hg19.chrM.fa.gz 2>&1 | grep -v "kent source version" > test2.txt 2>&1
-	@zdiff -q test2.txt expected/test2.txt.gz
+	@${findMotif} -verbose=2 -motif=GGGTTTAGTA hg19.chrM.fa.gz 2>&1 | grep -v "kent source version" > test2.txt 2>&1
+	@diff -q test2.txt <(gunzip -c expected/test2.txt.gz)
 	@ rm -f test2.txt
 
 test3:
-	@findMotif -misMatch=2 -verbose=2 -motif=TACTAAACCC hg19.chrM.fa.gz 2>&1 | grep -v "kent source version"  > test3.txt 2>&1
-	@zdiff -q test3.txt expected/test3.txt.gz
+	@${findMotif} -misMatch=2 -verbose=2 -motif=TACTAAACCC hg19.chrM.fa.gz 2>&1 | grep -v "kent source version"  > test3.txt 2>&1
+	@diff -q test3.txt <(gunzip -c expected/test3.txt.gz)
 	@ rm -f test3.txt
 
 test4:
-	@findMotif -misMatch=2 -verbose=2 -motif=GGGTTTAGTA hg19.chrM.fa.gz 2>&1 | grep -v "kent source version" > test4.txt 2>&1
-	@zdiff -q test4.txt expected/test4.txt.gz
+	@${findMotif} -misMatch=2 -verbose=2 -motif=GGGTTTAGTA hg19.chrM.fa.gz 2>&1 | grep -v "kent source version" > test4.txt 2>&1
+	@diff -q test4.txt <(gunzip -c expected/test4.txt.gz)
 	@ rm -f test4.txt
 
 test5:
-	@findMotif -misMatch=2 -motif=TACTAAACCC hg19.chrM.fa.gz > test5.txt 2>&1
-	@zdiff -q test5.txt expected/test5.txt.gz
+	@${findMotif} -misMatch=2 -motif=TACTAAACCC hg19.chrM.fa.gz > test5.txt 2>&1
+	@diff -q test5.txt <(gunzip -c expected/test5.txt.gz)
 	@ rm -f test5.txt
 
 test6:
-	@findMotif -misMatch=2 -motif=GGGTTTAGTA hg19.chrM.fa.gz > test6.txt 2>&1
-	@zdiff -q test6.txt expected/test6.txt.gz
+	@${findMotif} -misMatch=2 -motif=GGGTTTAGTA hg19.chrM.fa.gz > test6.txt 2>&1
+	@diff -q test6.txt <(gunzip -c expected/test6.txt.gz)
 	@ rm -f test6.txt
 
 test7:
-	@findMotif -misMatch=3 -verbose=2 -motif=GGGTTTAGTA hg19.chrM.fa.gz 2>&1 | grep -v "kent source version" > test7.txt 2>&1
-	@zdiff -q test7.txt expected/test7.txt.gz
+	@${findMotif} -misMatch=3 -verbose=2 -motif=GGGTTTAGTA hg19.chrM.fa.gz 2>&1 | grep -v "kent source version" > test7.txt 2>&1
+	@diff -q test7.txt <(gunzip -c expected/test7.txt.gz)
 	@ rm -f test7.txt
 
 test8:
-	@findMotif -misMatch=3 -motif=GGGTTTAGTA hg19.chrM.fa.gz > test8.txt 2>&1
-	@zdiff -q test8.txt expected/test8.txt.gz
+	@${findMotif} -misMatch=3 -motif=GGGTTTAGTA hg19.chrM.fa.gz > test8.txt 2>&1
+	@diff -q test8.txt <(gunzip -c expected/test8.txt.gz)
 	@ rm -f test8.txt
 
 # with error conditions
 
 test9:
-	@findMotif -misMatch=3 -motif=GGG hg19.chrM.fa.gz > test9.txt 2>&1 || true
-	@zdiff -q test9.txt expected/test9.txt.gz
+	@${findMotif} -misMatch=3 -motif=GGG hg19.chrM.fa.gz > test9.txt 2>&1 || true
+	@diff -q test9.txt <(gunzip -c expected/test9.txt.gz)
 	@rm -f test9.txt
 
 test10:
-	@findMotif -misMatch=3 -motif=TTACATAGTACATAAAGTCATTTACCGTACATA hg19.chrM.fa.gz > test10.txt 2>&1 || true
-	@zdiff -q test10.txt expected/test10.txt.gz
+	@${findMotif} -misMatch=3 -motif=TTACATAGTACATAAAGTCATTTACCGTACATA hg19.chrM.fa.gz > test10.txt 2>&1 || true
+	@diff -q test10.txt <(gunzip -c expected/test10.txt.gz)
 	@rm -f test10.txt
 
 test11:
-	@findMotif -misMatch=3 -motif=TACATAGTACATAAAGTCATTTACCGTACATA hg19.chrM.fa.gz > test11.txt 2>&1
-	@zdiff -q test11.txt expected/test11.txt.gz
+	@${findMotif} -misMatch=3 -motif=TACATAGTACATAAAGTCATTTACCGTACATA hg19.chrM.fa.gz > test11.txt 2>&1
+	@diff -q test11.txt <(gunzip -c expected/test11.txt.gz)
 	@rm -f test11.txt
 
 
 clean:
 	rm -f test*.txt