Question: Error with Operate on Genomics Interval Subtract Tool in Galaxy
gravatar for courtneys
3.6 years ago by
United States
courtneys0 wrote:

I keep getting errors when using the Subtract tool under the Operate On Genomic Intervals tools in Galaxy.  

Traceback (most recent call last):
  File "/nfs/software/galaxy/tools/new_operations/", line 23, in <module>
    from import *
  File "/nfs/software/galaxy/lib/galaxy/tools/", line 20, in <module>
    from parameters import *
  File "/nfs/software/galaxy/lib/galaxy/tools/parameters/", line 5, in <module>
    from basic import *
  File "/nfs/software/galaxy/lib/galaxy/tools/parameters/", line 1827, in <module>
    mod = __import__(module, fromlist=[classname])
  File "/nfs/software/galaxy/lib/galaxy/tools/parameters/globus/", line 7, in <module>
    from .oauth import OAuthAccessToken
  File "/nfs/software/galaxy/lib/galaxy/tools/parameters/globus/", line 8, in <module>
    from galaxy.web.framework.ext.globus import storage
  File "/nfs/software/galaxy/lib/galaxy/web/framework/ext/globus/", line 1, in <module>
    from . import (
  File "/nfs/software/galaxy/lib/galaxy/web/framework/ext/globus/middleware/", line 3, in <module>
    from .auth import UserAuthentication
  File "/nfs/software/galaxy/lib/galaxy/web/framework/ext/globus/middleware/", line 12, in <module>
    import nexus
  File "/mnt/galaxyTools/tools/pymodules/python2.7/lib/python/nexus_client-0.0.1-py2.7.egg/nexus/", line 1, in <module>
    from nexus.go_rest_client import GlobusOnlineRestClient
  File "/mnt/galaxyTools/tools/pymodules/python2.7/lib/python/nexus_client-0.0.1-py2.7.egg/nexus/", line 33, in <module>
    import nexus.token_utils as token_utils
  File "/mnt/galaxyTools/tools/pymodules/python2.7/lib/python/nexus_client-0.0.1-py2.7.egg/nexus/", line 20, in <module>
    import rsa
ImportError: No module named rsa


I am using two BED files that are both in interval format after running MACS, so I don't know what I am doing wrong, and I am not sure how to interpret this error message

galaxy subtract gobs • 1.0k views
ADD COMMENTlink modified 3.6 years ago by Jennifer Hillman Jackson25k • written 3.6 years ago by courtneys0
gravatar for Jennifer Hillman Jackson
3.6 years ago by
United States
Jennifer Hillman Jackson25k wrote:


The first thing to check is your python path. It looks like you are working on a cloud Galaxy. Did you use Cloud Launch to start the instance up? Did you change anything to the configuration files? Has any tool run successfully?

Thanks, Jen, Galaxy team

ADD COMMENTlink written 3.6 years ago by Jennifer Hillman Jackson25k
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