Hello Richard, this issue has been solved, if you update the tool it should work as expected. Details are available here: https://biostar.usegalaxy.org/p/15974/
Thank you for using Galaxy Martin On Tue, Dec 1, 2015 at 5:28 PM Poole, Richard <r.po...@ucl.ac.uk> wrote: > 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.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 > > 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) > > ___________________________________________________________ > Please keep all replies on the list by using "reply all" > in your mail client. To manage your subscriptions to this > and other Galaxy lists, please use the interface at: > https://lists.galaxyproject.org/ > > To search Galaxy mailing lists use the unified search at: > http://galaxyproject.org/search/mailinglists/
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