diff --git a/var/spack/repos/builtin/packages/gapfiller/package.py b/var/spack/repos/builtin/packages/gapfiller/package.py
index 442658903f009f4d95b16220021d58cb3b951c0f..c2fa5b025e7dfc174cf0feb93ce6ee709e303556 100644
--- a/var/spack/repos/builtin/packages/gapfiller/package.py
+++ b/var/spack/repos/builtin/packages/gapfiller/package.py
@@ -33,7 +33,7 @@ def url_for_version(self, version):
 
     def patch(self):
         with working_dir('.'):
-            files = glob.iglob("*.pl")
+            files = glob.glob("*.pl") + glob.glob('bwa/*.pl')
             for file in files:
                 change = FileFilter(file)
                 change.filter('usr/bin/perl', 'usr/bin/env perl')