Latest
Open
RNA-Seq
ChIP-Seq
SNP
Assembly
Forum
Planet
All »
Home
Log In
Question: best way to address module already imported
0
gravatar for Brad Langhorst
4.5 years ago by
Brad Langhorst • 100
United States
Brad Langhorst • 100 wrote:
rSeqC seems to ship with it's own version of bx...

but this is screwing up other stuff.

What's the best approach to fix it?

/mnt/galaxy/data/galaxy/galaxy-dist/lib/galaxy/__init__.py:79: UserWarning: Module bx was already imported from /mnt/galaxy/data/galaxy/sw/lib/python2.7/site-packages/RSeQC-2.3.9-py2.7-linux-x86_64.egg/bx/__init__.pyc, but /mnt/galaxy/data/galaxy/galaxy-dist/eggs/bx_python-0.7.1_7b95ff194725-py2.7-linux-x86_64-ucs2.egg is being added to sys.path
  self.check_version_conflict()
rseqc • 1.2k views
ADD COMMENT • link •
modified 4.5 years ago • written 4.5 years ago by Brad Langhorst • 100

Hi Brad,

have you tried to run Galaxy in a virtual_env? The wiki has a good description about that.

 

ADD REPLY • link written 4.5 years ago by Bjoern Gruening ♦ 5.1k

Yes, I'm using a dedicated virtual env for galaxy already - I think the problem is that rseqc (a toolshed tool) has installed it's own local copy of bx in addition to the bx from galaxy.  I bet the rseqc tool has the same warning, but the tool is not configured to be in an error state if there is stderr output.

Maybe this is an rseqc tool bug?

ADD REPLY • link modified 4.5 years ago • written 4.5 years ago by Brad Langhorst • 100
0
gravatar for Brad Langhorst
4.5 years ago by
Brad Langhorst • 100
United States
Brad Langhorst • 100 wrote:

I've "resolved" this by adding a stdio section to the interval subtraction tool so that the warning about multiple bx versions is ignored.

I don't love it, but at least I can run the tool now.

 

 
ADD COMMENT • link written 4.5 years ago by Brad Langhorst • 100
Please log in to add an answer.

Similar posts • Search »

Content
Help
Access
Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 171 users visited in the last hour