diff --git a/analysis/R/alternative.R b/analysis/R/alternative.R
old mode 100644
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diff --git a/analysis/R/association.R b/analysis/R/association.R
old mode 100644
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diff --git a/analysis/R/association_test.R b/analysis/R/association_test.R
old mode 100644
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diff --git a/analysis/R/decode.R b/analysis/R/decode.R
old mode 100644
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diff --git a/analysis/R/decode_ngrams.R b/analysis/R/decode_ngrams.R
old mode 100644
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diff --git a/analysis/R/encode.R b/analysis/R/encode.R
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diff --git a/analysis/R/fast_em.R b/analysis/R/fast_em.R
old mode 100644
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diff --git a/analysis/R/ngrams_simulation.R b/analysis/R/ngrams_simulation.R
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diff --git a/analysis/R/read_input.R b/analysis/R/read_input.R
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diff --git a/analysis/R/simulation.R b/analysis/R/simulation.R
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diff --git a/analysis/R/unknowns_test.R b/analysis/R/unknowns_test.R
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diff --git a/analysis/R/util.R b/analysis/R/util.R
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diff --git a/apps/rappor-analysis/server.R b/apps/rappor-analysis/server.R
old mode 100644
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diff --git a/apps/rappor-analysis/ui.R b/apps/rappor-analysis/ui.R
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diff --git a/apps/rappor-sim/server.R b/apps/rappor-sim/server.R
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diff --git a/apps/rappor-sim/ui.R b/apps/rappor-sim/ui.R
old mode 100644
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diff --git a/bin/decode-assoc b/bin/decode-assoc
old mode 100755
new mode 100644
diff --git a/bin/decode-dist b/bin/decode-dist
old mode 100755
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diff --git a/bin/hash-candidates b/bin/hash-candidates
old mode 100755
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diff --git a/bin/sum-bits b/bin/sum-bits
old mode 100755
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diff --git a/client/python/rappor.py b/client/python/rappor.py
old mode 100644
new mode 100755
diff --git a/client/python/rappor_test.py b/client/python/rappor_test.py
index 66e90ee..1aa6288 100755
--- a/client/python/rappor_test.py
+++ b/client/python/rappor_test.py
@@ -17,7 +17,6 @@
 """
 rappor_test.py: Tests for rappor.py
 """
-
 import cStringIO
 import copy
 import math
@@ -102,14 +101,14 @@ class MockRandom(object):
   def __init__(self, cycle, params):
     self.p_gen = MockRandomCall(params.prob_p, cycle, params.num_bloombits)
     self.q_gen = MockRandomCall(params.prob_q, cycle, params.num_bloombits)
-    
+
 class MockRandomCall:
   def __init__(self, prob, cycle, num_bits):
     self.cycle = cycle
     self.n = len(self.cycle)
     self.prob = prob
     self.num_bits = num_bits
-    
+
   def __call__(self):
     counter = 0
     r = 0
diff --git a/pipeline/tools-lib.sh b/pipeline/tools-lib.sh
old mode 100644
new mode 100755
diff --git a/pipeline/util.py b/pipeline/util.py
old mode 100644
new mode 100755
diff --git a/tests/compare_dist.R b/tests/compare_dist.R
index 65074c4..eb6521d 100755
--- a/tests/compare_dist.R
+++ b/tests/compare_dist.R
@@ -80,6 +80,7 @@ RunRappor <- function(prefix_case, prefix_instance, ctx) {
   counts <- ReadCountsFile(c, ctx$params)
 
   m <- paste0(prefix_case, '_map.csv')
+
   # Switch to LoadMapFile if want to cache the result
   map <- ReadMapFile(m, ctx$params)
 
diff --git a/tests/fastrand.py b/tests/fastrand.py
old mode 100644
new mode 100755
diff --git a/tests/fastrand_test.py b/tests/fastrand_test.py
index 117c405..d3bdbf1 100755
--- a/tests/fastrand_test.py
+++ b/tests/fastrand_test.py
@@ -17,7 +17,6 @@
 """
 fastrand_test.py: Tests for _fastrand extension module.
 """
-
 import unittest
 
 import _fastrand  # module under test
diff --git a/tests/gen_counts.R b/tests/gen_counts.R
old mode 100644
new mode 100755
diff --git a/tests/rappor_sim.py b/tests/rappor_sim.py
index acb6139..66c7fc3 100755
--- a/tests/rappor_sim.py
+++ b/tests/rappor_sim.py
@@ -111,6 +111,7 @@ def GenAssocTestdata(params1, params2, irr_rand, assoc_testdata_count,
   for i in xrange(n):
     for v1, v2 in rows:
       client_str = 'c%d' % report_index
+
       # randint(a, b) gives i such that a <= i <= b
       cohort = random.randint(0, params1.num_cohorts - 1)
 
diff --git a/tests/setup.py b/tests/setup.py
old mode 100644
new mode 100755
diff --git a/util.sh b/util.sh
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