diff --git a/easybuild/easyblocks/b/blat.py b/easybuild/easyblocks/b/blat.py
old mode 100755
new mode 100644
diff --git a/easybuild/easyblocks/b/bwa.py b/easybuild/easyblocks/b/bwa.py
old mode 100755
new mode 100644
diff --git a/easybuild/easyblocks/c/chimera.py b/easybuild/easyblocks/c/chimera.py
old mode 100755
new mode 100644
diff --git a/easybuild/easyblocks/generic/binariestarball.py b/easybuild/easyblocks/generic/binariestarball.py
index f6a56aec0a8..82246b9a382 100644
--- a/easybuild/easyblocks/generic/binariestarball.py
+++ b/easybuild/easyblocks/generic/binariestarball.py
@@ -32,6 +32,7 @@
 import stat
 
 from easybuild.easyblocks.generic.tarball import Tarball
+from easybuild.framework.easyconfig import CUSTOM
 from easybuild.tools.build_log import EasyBuildError
 from easybuild.tools.filetools import adjust_permissions
 
@@ -40,21 +41,40 @@ class BinariesTarball(Tarball):
     """
     Support for installing a tarball of binaries
     """
+    @staticmethod
+    def extra_options(extra_vars=None):
+        """
+        Define list of files to be copied during the installation process
+        """
+        extra_vars = Tarball.extra_options(extra_vars)
+        # Allow specification of files to copy explicitly.
+        # If files_to_copy is a zero-length list, all files (but not
+        # directories, etc.) in start_dir will be copied with their
+        # current names.
+        extra_vars.update({
+            'files_to_copy': [None, "List of optional (source_file, destination_file) tuples", CUSTOM,]
+        })
+        return extra_vars
 
     def install_step(self):
         """Install by copying unzipped binaries to 'bin' subdir of installation dir, and fixing permissions."""
 
         bindir = os.path.join(self.installdir, 'bin')
+        items_to_copy = []
         try:
             os.makedirs(bindir)
-            for item in os.listdir(self.cfg['start_dir']):
+            if self.cfg['files_to_copy'] is None:
+                for item in os.listdir(self.cfg['start_dir']):
+                    items_to_copy.append((os.path.join(self.cfg['start_dir'], item), item))
+            else:
+                items_to_copy.append(os.path.join(self.cfg['start_dir'], item) for item in self.cfg['files_to_copy'])
+            for (item, destname) in items_to_copy:
                 if os.path.isfile(item):
-                    shutil.copy2(os.path.join(self.cfg['start_dir'], item), bindir)
+                    shutil.copy2(item, os.path.join(bindir, destname))
                     # make sure binary has executable permissions
-                    adjust_permissions(os.path.join(bindir, item), stat.S_IXUSR|stat.S_IXGRP|stat.S_IXOTH, add=True)
-                    self.log.debug("Copied %s to %s and fixed permissions" % (item, bindir))
+                    adjust_permissions(os.path.join(bindir, destname), stat.S_IXUSR|stat.S_IXGRP|stat.S_IXOTH, add=True)
+                    self.log.debug("Copied %s to %s and fixed permissions", item, bindir)
                 else:
-                    self.log.warning("Skipping non-file %s in %s, not copying it." % (item, self.cfg['start_dir']))
+                    self.log.warning("%s: not a file. Skipping.", item)
         except OSError, err:
-            raise EasyBuildError("Copying binaries in %s to install dir 'bin' failed: %s", self.cfg['start_dir'], err)
-
+            raise EasyBuildError("Copying binaries to install dir 'bin' failed: %s", err)
diff --git a/easybuild/easyblocks/generic/cmdcp.py b/easybuild/easyblocks/generic/cmdcp.py
old mode 100755
new mode 100644
diff --git a/easybuild/easyblocks/generic/makecp.py b/easybuild/easyblocks/generic/makecp.py
old mode 100755
new mode 100644
diff --git a/easybuild/easyblocks/m/modeller.py b/easybuild/easyblocks/m/modeller.py
old mode 100755
new mode 100644