ImportError: No module named utils.gff_util using Genomics Operations "subtract" tool

Question: ImportError: No module named utils.gff_util using Genomics Operations "subtract" tool

2.8 years ago by

United States

Lance Parsons • 110 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 • 1.6k views

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modified 2.8 years ago by Philipp.rathert • 30 • written 2.8 years ago by Lance Parsons • 110

2.8 years ago by

Lance Parsons • 110

United States

Lance Parsons • 110 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 COMMENT • link modified 2.8 years ago • written 2.8 years ago by Lance Parsons • 110

2.8 years 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 COMMENT • link written 2.8 years 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 REPLY • link written 2.8 years ago by Lance Parsons • 110

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

ADD REPLY • link written 2.8 years ago by Dave B. ♦ 410

2.8 years ago by

Philipp.rathert • 30

Germany

Philipp.rathert • 30 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 COMMENT • link modified 2.8 years ago • written 2.8 years ago by Philipp.rathert • 30

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

ADD REPLY • link modified 2.8 years ago • written 2.8 years ago by Lance Parsons • 110

you refer to package_bx_python_0_7 and package_galaxy_ops_1_0_0?

ADD REPLY • link written 2.8 years ago by Philipp.rathert • 30

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

ADD REPLY • link modified 2.8 years ago • written 2.8 years ago by Lance Parsons • 110

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

ADD REPLY • link written 2.8 years ago by Philipp.rathert • 30

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

ADD REPLY • link written 2.8 years ago by Lance Parsons • 110

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