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.poole@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/