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Convert BED to Feature Location Index breaks when "preserve_python_environment = legacy_only"

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Convert BED to Feature Location Index breaks when "preserve_python_environment = legacy_only"

Hans-Rudolf Hotz
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
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Re: Convert BED to Feature Location Index breaks when "preserve_python_environment = legacy_only"

Hans-Rudolf Hotz

...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
>
>
>
>
___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
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