Question: ImportError: No module named utils.gff_util using Genomics Operations "subtract" tool
0
gravatar for Lance Parsons
22 months ago by
Lance Parsons110
United States
Lance Parsons110 wrote:

I'm running into an error running the "subtract" tool for genomics intervals:

Traceback (most recent call last):
  File "/galaxy/shed_tools/toolshed.g2.bx.psu.edu/repos/devteam/subtract/c19a2a29c561/subtract/gops_subtract.py", line 21, in <module>
    from utils.gff_util import GFFFeature, GFFReaderWrapper, convert_bed_coords_to_gff
ImportError: No module named utils.gff_util

The dependencies (package_bx_python_0_7 and package_galaxy_ops_1_0_0) seem to be properly installed.

This error was reported earlier on the Galaxy-Development list, but I haven't seen any replies.

software error • 1.0k views
ADD COMMENTlink modified 22 months ago by Philipp.rathert30 • written 22 months ago by Lance Parsons110
2
gravatar for Lance Parsons
22 months ago by
Lance Parsons110
United States
Lance Parsons110 wrote:

We tracked down this issue to a bug in the tool (missing python lib). It's since been fixed in the toolshed, see https://github.com/galaxyproject/tools-devteam/pull/335.

To fix the issues, users should update the flanking_features, intersect, and subtract tools.

ADD COMMENTlink modified 22 months ago • written 22 months ago by Lance Parsons110
0
gravatar for Dave B.
22 months ago by
Dave B.410
United States
Dave B.410 wrote:

Lance,

It's possible that you're using an older revision of package_galaxy_ops_1_0_0, the first thing I'd try is updating that repository and reinstalling its tool dependency.

ADD COMMENTlink written 22 months ago by Dave B.410

There were no updates to either package_galaxy_ops_1_0_0 or package_bx_python_0_7. However, I don't think that either of those packages exposes this module. It seems to be `galaxy.datatypes.util/gff_util.py` that is supposed to be exposed as utils.gff_util according to @dannon. I did try reinstalling, but to no avail.

ADD REPLYlink written 22 months ago by Lance Parsons110

Shucks and darn. Ok, I'll have a look at the tool itself.

ADD REPLYlink written 22 months ago by Dave B.410
0
gravatar for Philipp.rathert
22 months ago by
Germany
Philipp.rathert30 wrote:

Dear All,

 

I think I have a similar mistake when using intersect:

it would be great if somebody has an idea how to fix this.

Traceback (most recent call last):
File "/shed_tools/toolshed.g2.bx.psu.edu/repos/devteam/intersect/5f72be09cfd3/intersect/gops_intersect.py", line 21, in <module>
from utils.gff_util import GFFFeature, GFFReaderWrapper, convert_bed_coords_to_gffImportError: No module named utils.gff_util
ADD COMMENTlink modified 22 months ago • written 22 months ago by Philipp.rathert30

The latest update (4:8ddabc73af92) should fix this (see my earlier answer). Let us know if you still have issues after an update.

ADD REPLYlink modified 22 months ago • written 22 months ago by Lance Parsons110

you refer to package_bx_python_0_7 and package_galaxy_ops_1_0_0?

ADD REPLYlink written 22 months ago by Philipp.rathert30

Sorry, I should have been more clear, you need to update the tools themselves (subtract, intersect, flanking_features). I've edited my answer.

ADD REPLYlink modified 22 months ago • written 22 months ago by Lance Parsons110

ok got it, was confused since there was no update uption mentioned under Admin-manage installed tools...

ADD REPLYlink written 22 months ago by Philipp.rathert30

You'll need to click on "Update tool shed status" to check for new updates.

ADD REPLYlink written 22 months ago by Lance Parsons110
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