diff --git a/configure.ac b/configure.ac
index 23fbf5c6e4c4211379986a4a9c951892d044713c..09346ca9083e18df6d69ea09d23df62e17bcde09 100644
--- a/configure.ac
+++ b/configure.ac
@@ -461,6 +461,12 @@ AM_CONDITIONAL([HAVE_DOXYGEN], [test "$ac_cv_path_ac_pt_DX_DOXYGEN" != ""])
 
 # Handle .in files.
 AC_CONFIG_FILES([Makefile src/Makefile examples/Makefile doc/Makefile doc/Doxyfile tests/Makefile])
+AC_CONFIG_FILES([tests/testReading.sh], [chmod +x tests/testReading.sh])
+AC_CONFIG_FILES([tests/testPair.sh], [chmod +x tests/testPair.sh])
+AC_CONFIG_FILES([tests/testPairPerturbed.sh], [chmod +x tests/testPairPerturbed.sh])
+AC_CONFIG_FILES([tests/test27cells.sh], [chmod +x tests/test27cells.sh])
+AC_CONFIG_FILES([tests/test27cellsPerturbed.sh], [chmod +x tests/test27cellsPerturbed.sh])
+AC_CONFIG_FILES([tests/testParser.sh], [chmod +x tests/testParser.sh])
 
 # Report general configuration.
 AC_MSG_RESULT([
diff --git a/tests/test27cells.sh b/tests/test27cells.sh.in
similarity index 52%
rename from tests/test27cells.sh
rename to tests/test27cells.sh.in
index 0afdc32c95397ce76190e847bdcd04a0b079ef78..b55657664788ee6e005b5c39f7bd226351747c09 100755
--- a/tests/test27cells.sh
+++ b/tests/test27cells.sh.in
@@ -3,6 +3,6 @@ rm brute_force_27_standard.dat swift_dopair_27_standard.dat
 
 ./test27cells -p 6 -r 1 -d 0 -f standard
 
-python difffloat.py brute_force_27_standard.dat swift_dopair_27_standard.dat tolerance.dat 6
+python @srcdir@/difffloat.py brute_force_27_standard.dat swift_dopair_27_standard.dat @srcdir@/tolerance.dat 6
 
 exit $?
diff --git a/tests/test27cellsPerturbed.sh b/tests/test27cellsPerturbed.sh.in
similarity index 53%
rename from tests/test27cellsPerturbed.sh
rename to tests/test27cellsPerturbed.sh.in
index a553a2553e92cedee7c2c0679d231ec9d982fc28..3d7574f9e9fa01697bfd85097f223724e65b2408 100755
--- a/tests/test27cellsPerturbed.sh
+++ b/tests/test27cellsPerturbed.sh.in
@@ -3,6 +3,6 @@ rm brute_force_27_perturbed.dat swift_dopair_27_perturbed.dat
 
 ./test27cells -p 6 -r 1 -d 0.1 -f perturbed
 
-python difffloat.py brute_force_27_perturbed.dat swift_dopair_27_perturbed.dat tolerance.dat 6
+python @srcdir@/difffloat.py brute_force_27_perturbed.dat swift_dopair_27_perturbed.dat @srcdir@/tolerance.dat 6
 
 exit $?
diff --git a/tests/testPair.sh b/tests/testPair.sh.in
similarity index 52%
rename from tests/testPair.sh
rename to tests/testPair.sh.in
index f6f505e56a2c7a5c3cff0ec04bd871278634193c..e719aeec4a96c87eb2924f928b4b10dd27c51a82 100755
--- a/tests/testPair.sh
+++ b/tests/testPair.sh.in
@@ -3,6 +3,6 @@ rm brute_force_standard.dat swift_dopair_standard.dat
 
 ./testPair -p 6 -r 1 -d 0 -f standard
 
-python difffloat.py brute_force_standard.dat swift_dopair_standard.dat tolerance.dat
+python @srcdir@/difffloat.py brute_force_standard.dat swift_dopair_standard.dat @srcdir@/tolerance.dat
 
 exit $?
diff --git a/tests/testPairPerturbed.sh b/tests/testPairPerturbed.sh.in
similarity index 53%
rename from tests/testPairPerturbed.sh
rename to tests/testPairPerturbed.sh.in
index 544ba1b032da8426c065dcfb2ce3ee554c5e76a1..d94a040d42c2e274d06592549302c0748ddb2793 100755
--- a/tests/testPairPerturbed.sh
+++ b/tests/testPairPerturbed.sh.in
@@ -3,6 +3,6 @@ rm brute_force_perturbed.dat swift_dopair_perturbed.dat
 
 ./testPair -p 6 -r 1 -d 0.1 -f perturbed
 
-python difffloat.py brute_force_perturbed.dat swift_dopair_perturbed.dat tolerance.dat
+python @srcdir@/difffloat.py brute_force_perturbed.dat swift_dopair_perturbed.dat @srcdir@/tolerance.dat
 
 exit $?
diff --git a/tests/testParser.sh b/tests/testParser.sh
deleted file mode 100755
index 53d2bbe4e0230032666ace228449f913f03e0464..0000000000000000000000000000000000000000
--- a/tests/testParser.sh
+++ /dev/null
@@ -1,4 +0,0 @@
-#!/bin/bash
-
-rm parser_output.yml
-./testParser testParserInput.yaml
diff --git a/tests/testParser.sh.in b/tests/testParser.sh.in
new file mode 100755
index 0000000000000000000000000000000000000000..6c62bc57c041576ea6e807a0a31052ee1dffb4db
--- /dev/null
+++ b/tests/testParser.sh.in
@@ -0,0 +1,4 @@
+#!/bin/bash
+
+rm parser_output.yml
+./testParser @srcdir@/testParserInput.yaml
diff --git a/tests/testReading.sh b/tests/testReading.sh
deleted file mode 100755
index a03a1438cd83de147fece10aa03ea3f7af66c7a4..0000000000000000000000000000000000000000
--- a/tests/testReading.sh
+++ /dev/null
@@ -1,5 +0,0 @@
-#!/bin/bash
-
-python makeInput.py
-./testReading
-
diff --git a/tests/testReading.sh.in b/tests/testReading.sh.in
new file mode 100755
index 0000000000000000000000000000000000000000..d9dde0ec9160183afcf7c4fe9c8061114aadef48
--- /dev/null
+++ b/tests/testReading.sh.in
@@ -0,0 +1,5 @@
+#!/bin/bash
+
+python @srcdir@/makeInput.py
+./testReading
+