update write permissions via in-built python functions

src/projects/spades/pipeline/spades_pipeline/support.py

@@ -925,6 +925,20 @@ def is_int(value):
         return False
 
 
+def add_user_write_permission_recursive(path):
+    s = os.stat(path)
+    os.chmod(path, s.st_mode | stat.S_IRWXU)
+    for root, dirs, files in os.walk(path):
+        for d in dirs:
+            d = os.path.join(root, d)
+            s = os.stat(d)
+            os.chmod(d, s.st_mode | stat.S_IRWXU)
+        for f in files:
+            f = os.path.join(root, f)
+            s = os.stat(d)
+            os.chmod(f, s.st_mode | stat.S_IRWXU)
+
+
 # shutil.copyfile does not copy any metadata (time and permission), so one
 # cannot expect preserve_mode = False and preserve_times = True to work.
 def copy_tree(src, dst, preserve_times=True, preserve_mode=True):
@@ -939,7 +953,7 @@ def copy_tree(src, dst, preserve_times=True, preserve_mode=True):
     # shutil.copytree preserves the timestamp, so we must update it afterwards.
     shutil.copytree(src, dst, copy_function = copy_fn)
     if not preserve_mode:
-        os.system('chmod -R u+w '+dst)
+        add_user_write_permission_recursive(dst)
 
     if not preserve_times:
         for dirpath, _, filenames in os.walk(dst):