diff --git a/tools/filters/gff/gff_filter_by_attribute.py b/tools/filters/gff/gff_filter_by_attribute.py
index cd6600cf916..3d4319bc152 100644
--- a/tools/filters/gff/gff_filter_by_attribute.py
+++ b/tools/filters/gff/gff_filter_by_attribute.py
@@ -6,8 +6,9 @@
 from __future__ import division
 
 import sys
-from json import loads
+
 from ast import Module, parse, walk
+from json import loads
 
 AST_NODE_TYPE_WHITELIST = [
     'Expr', 'Load', 'Str', 'Num', 'BoolOp', 'Compare', 'And', 'Eq', 'NotEq',
@@ -152,6 +153,7 @@ def check_expression( text ):
 
     return True
 
+
 #
 # Helper functions.
 #
diff --git a/tools/filters/gff/gff_filter_by_feature_count.py b/tools/filters/gff/gff_filter_by_feature_count.py
index 778527972bc..d0e65caa9f5 100644
--- a/tools/filters/gff/gff_filter_by_feature_count.py
+++ b/tools/filters/gff/gff_filter_by_feature_count.py
@@ -5,12 +5,15 @@ Filter a gff file using a criterion based on feature counts for a transcript.
 Usage:
 %prog input_name output_name feature_name condition
 """
+from __future__ import print_function
+
 import sys
 
+from ast import Module, parse, walk
+
 from bx.intervals.io import GenomicInterval
 
 from galaxy.datatypes.util.gff_util import GFFReaderWrapper
-from ast import Module, parse, walk
 
 AST_NODE_TYPE_WHITELIST = [
     'Expr', 'Load', 'Str', 'Num', 'BoolOp', 'Compare', 'And', 'Eq', 'NotEq',
@@ -137,7 +140,7 @@ def __main__():
             except:
                 number = None
             if empty != "" or not number:
-                print >> sys.stderr, "Invalid condition: %s, cannot filter." % condition
+                print("Invalid condition: %s, cannot filter." % condition, file=sys.stderr)
                 return
             break
 
@@ -173,7 +176,7 @@ def __main__():
         ( kept_features, i, float(kept_features) / i * 100.0, feature_name + condition )
     if skipped_lines > 0:
         info_msg += "Skipped %d blank/comment/invalid lines starting with line #%d." % ( skipped_lines, first_skipped_line )
-    print info_msg
+    print(info_msg)
 
 if __name__ == "__main__":
     __main__()
diff --git a/tox.ini b/tox.ini
index 561d0637f5d..c4822638555 100644
--- a/tox.ini
+++ b/tox.ini
@@ -41,7 +41,7 @@ whitelist_externals = bash
 skip_install = True
 deps =
     flake8
-    flake8-import-order>=0.9
+    flake8-import-order==0.9
 
 [testenv:py27-lint-imports-include-list]
 commands = bash .ci/flake8_wrapper_imports.sh
@@ -49,7 +49,7 @@ whitelist_externals = bash
 skip_install = True
 deps =
     flake8==3.0.4
-    flake8-import-order>=0.9
+    flake8-import-order==0.9
 
 [testenv:qunit]
 commands = bash run_tests.sh -q