add @nsheff changes from dockerfix and avoid merge conflict

databio · Jun 20, 2019 · 27cb5df · 27cb5df
1 parent 6e6e6c4
commit 27cb5df
Showing 1 changed file with 7 additions and 0 deletions.
diff --git a/pypiper/manager.py b/pypiper/manager.py
@@ -1823,6 +1823,13 @@ def get_container(self, image, mounts):
         for mnt in mounts:
             absmnt = os.path.abspath(mnt)
             cmd += " -v " + absmnt + ":" + absmnt
+        cmd += " -v {cwd}:{cwd} --workdir={cwd}".format(cwd=os.getcwd())
+        cmd += " --user={uid}".format(uid=os.getuid())
+        cmd += " --volume=/etc/group:/etc/group:ro"
+        cmd += " --volume=/etc/passwd:/etc/passwd:ro"
+        cmd += " --volume=/etc/shadow:/etc/shadow:ro"
+        cmd += " --volume=/etc/sudoers.d:/etc/sudoers.d:ro"
+        cmd += " --volume=/tmp/.X11-unix:/tmp/.X11-unix:rw"
         cmd += " " + image
         container = self.checkprint(cmd).rstrip()
         self.container = container