There appears to be some inconsistent use of tempfile.mkstemp() within
upload.py that causes problems when users import data files to galaxy
from a cluster directory via the upload process and import/temp/dataset
directories are on different file systems.
The issue manifests when Galaxy's job
Iyad,
Thanks for chiming in. We looked at the patch you had posted, but we run on a
cluster galaxy shares with other apps, so the galaxy user does not have sudo
outside of the galaxy head-node.
The upload.py code you posted, therefore does not work for us.
Therefore, we're also looking at a
We've considered the sudo solution, but it opens the window to other
bugs giving galaxy the power to change ownership of other files in our
shared user cluster environment. We could isolate the power to a script
but then we still need to monitor this code closely. We'd prefer not to
introduce
