Mercurial > repos > jdv > albacore

diff albacore_1D.py @ 3:d561e3f9ccbb draft
planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit d8cc434bd1704b2834f89b7d91370f356e3ac85a
author: jdv
date: Tue, 03 Oct 2017 20:12:09 -0400
parents: 0a4f83207e53
children: 8a9f61d08201
--- a/albacore_1D.py	Fri Sep 08 10:14:40 2017 -0400
+++ b/albacore_1D.py	Tue Oct 03 20:12:09 2017 -0400
@@ -7,7 +7,6 @@
 import shutil
 import h5py
 import numpy as np
-import tarfile
 from distutils.util import strtobool
 
 def main():
@@ -93,8 +92,15 @@
         if not os.path.exists(in_dir):
             os.makedirs(in_dir)
 
-        tar = tarfile.open(fn, mode='r')
-        tar.extractall(path=in_dir)
+        # python's tarfile interface does not sanitize file paths within
+        # tarballs, which can be a big security risk. GNU tar does sanitize by
+        # default, so it's easier/safer here just to call the system tar
+        subprocess.call([
+            "tar",
+            "-xf",
+            fn,
+            "-C",
+            in_dir])
 
         files = glob.glob(
             os.path.join(in_dir, "**", "*.fast5"),