Fix for package managers storing files in read-only

update write permissions via in-built python functions

fix: do not give exec permissions

fix whatever typo is was

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_IWUSR | stat.S_IRUSR)
+ 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_IWUSR | stat.S_IRUSR)
+ for f in files:
+ f = os.path.join(root, f)
+ s = os.stat(d)
+ os.chmod(f, s.st_mode | stat.S_IWUSR | stat.S_IRUSR)
+
+
 # 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):
@@ -938,10 +952,12 @@ 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:
+ add_user_write_permission_recursive(dst)
 
  if not preserve_times:
  for dirpath, _, filenames in os.walk(dst):
  os.utime(dirpath, None)
  for file in filenames:
  os.utime(os.path.join(dirpath, file), None)
- 
+