Convert BED to Feature Location Index breaks when "preserve_python_environment = legacy_only"
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): File "/***/galaxy_dev/***/galaxy/lib/galaxy/datatypes/converters/interval_to_fli.py", 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 -- Hans-Rudolf Hotz, PhD Bioinformatics Support Friedrich Miescher Institute for Biomedical Research Maulbeerstrasse 66 4058 Basel/Switzerland
...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. Hans-Rudolf 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): File "/***/galaxy_dev/***/galaxy/lib/galaxy/datatypes/converters/interval_to_fli.py", 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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Hans-Rudolf Hotz