Mercurial > repos > jdv > nanonet

diff nanonet_1D.py @ 2:3f35881c2e25 draft default tip
planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanonet commit d8cc434bd1704b2834f89b7d91370f356e3ac85a
author: jdv
date: Tue, 03 Oct 2017 20:51:59 -0400
parents: decd5688d719
--- a/nanonet_1D.py	Fri Sep 08 11:03:35 2017 -0400
+++ b/nanonet_1D.py	Tue Oct 03 20:51:59 2017 -0400
@@ -2,7 +2,6 @@
 
 import sys, os
 import glob
-import tarfile
 import subprocess
 import shutil
 import h5py
@@ -28,8 +27,15 @@
         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"),