I just used the subtract tool (installed under Operate on Genomic Intervals) on my own Galaxy server for the first time in a very long time and got this error message from the tool:

Traceback (most recent call last):
  File "/Users/galaxy/shed_tools/toolshed.g2.bx.psu.edu/repos/devteam/subtract/c19a2a29c561/subtract/gops_subtract.py", line 16, in <module>
    from bx.intervals.io import GenomicInterval, NiceReaderWrapper
ImportError: No module named bx.intervals.io

So I uninstalled the intersect and subtract tools, plus the bx-python 0.7.1 package plus the galaxy-ops package and reinstalled both tools from the toolshed using the latest revisions of each from devteam. I now get this error message:

/Users/galaxy/galaxy-dist/lib/galaxy/__init__.py:63: UserWarning: Module bx was already imported from /Users/galaxy/galaxy-dist/tool-dependencies/bx-python/0.7.1/devteam/package_bx_python_0_7/2d0c08728bca/venv/lib/python2.7/site-packages/bx/__init__.pyc, but /Users/galaxy/galaxy-dist/eggs/bx_python-0.7.2-py2.7-macosx-10.6-intel-ucs2.egg is being added to sys.path
  self.check_version_conflict()
Traceback (most recent call last):
  File "/Users/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

I also then tried updating Galaxy to latest release 15.07 and even 15.10 which appeared in the git tag list as I writing this email, but no fix there - my Galaxy is running on a Mac OS X 10.10.5 Yosemite.

Any thoughts on how to resolve this problem?

Cheers,

Rich