...and indeed adding it to the "whitelist" (~/galaxy_dev/8090/galaxy/lib/galaxy/tools/_init__.py

solves the problem. I can keep 'preserve_python_environment = legacy_only'

I have made a pull request.


On 03/27/2017 04:38 PM, Hans-Rudolf Hotz wrote:
Hi All

I am in the process of updating our local galaxy servers to release 17.01.

Using the new release, I get the following error, when I try to display
a simple bed file in trackster:

Traceback (most recent call last):
line 20, in
     from galaxy.datatypes.util.gff_util import
convert_gff_coords_to_bed, GFFReaderWrapper, read_unordered_gtf
ImportError: No module named galaxy.datatypes.util.gff_util

When change 'preserve_python_environment = legacy_only' to
'preserve_python_environment = always' in "galaxy.ini" it works.

Looks like more tools need to be added to the "whitelist" ?

Regards, Hans-Rudolf

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