Hi all,
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.pyhttp://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.pyhttp://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
Does this suggest an incompatibility somehow with the the egg which is installed at startup and is versions 0.7.2 - I tried manually editing the egg file but could not switch that to 0.7.1
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
Richard J Poole PhD Wellcome Trust Fellow Department of Cell and Developmental Biology University College London 518 Rockefeller 21 University Street, London WC1E 6DE Office (518 Rockefeller): +44 20 7679 6577 (int. 46577) Lab (529 Rockefeller): +44 20 7679 6133 (int. 46133)