Question: bx version conflict from cluster tool
gravatar for Brad Langhorst
4.4 years ago by
United States
Brad Langhorst100 wrote:

When I run the cluster tool it prints this to stderr... which fails the step.

/mnt/galaxy/data/galaxy/galaxy-dist/lib/galaxy/ UserWarning: Module bx was already imported from /mnt/galaxy/data/galaxy/tool-deps/bx-python/0.7.1/devteam/package_bx_python_0_7/2d0c08728bca/venv/lib/python2.7/site-packages/bx/__init__.pyc, but /mnt/galaxy/data/galaxy/galaxy-dist/eggs/bx_python-0.7.2-py2.7-linux-x86_64-ucs2.egg is being added to sys.path


I've going to work around it by specifying a stdio block  instead, but how should I resolve the underlying conflicting bx version issue.

tool • 1.3k views
ADD COMMENTlink modified 4.4 years ago by Jennifer Hillman Jackson25k • written 4.4 years ago by Brad Langhorst100

That workaround is less than ideal :) not sure what to do about this though. Maybe we need to update Galaxy's version of this egg... what tool produces this error?

ADD REPLYlink written 4.3 years ago by jmchilton1.1k

Another solution would be to find the tools that actually need Galaxy's lib dir and have them assert something so the job script template only includes PYTHONPATH for those tools. Unless this is one of those tools.

ADD REPLYlink written 4.2 years ago by Nate Coraor3.2k
gravatar for Jennifer Hillman Jackson
4.4 years ago by
United States
Jennifer Hillman Jackson25k wrote:

Hi Brad,

I didn't check the mailing list to see if you explored the issue there yet. But you might try posting there to reach the dev community, the majority are using that venue still. That said, I did bring this post to the attention of our dev team later last week. A reply here is still a potential.

If you do/did come to a solution, through the dev list or other method, it would be great to post that back here. As a link if on the dev list (nabble or other) or if you have time for it, the actual solution written out (any source) to place it in the archives here as a searchable "A" post. You can answer your own Q's. Tthis applies to anyone who wishes to share learned solutions - more issue example "Q"'s with solutions "A"'s are always a good thing - one never knows what may be the key to unlock a future issue! Sometimes it is hard to know what the root cause is, and initial diagnostic clues can be interpreted many ways, by new and experienced alike.

Please know that dev questions are certainly welcome at Galaxy Biostar. While started for end-user Q's, we think the Biostar model is a great way to communicate and are letting the community as a whole (end users and dev alike) decide on the preferred forum going forward for support and general discussion. Any cross-over/transition takes early adaptors/advocates plus good measure of encouragement and patience :) Both may co-exit always, or not, we'll see!

Sorry I can't help more with the details, but while I can take a guess, I'd rather not head you down the wrong path and waste your time.

Best!! Jen, Galaxy team

ADD COMMENTlink modified 4.4 years ago • written 4.4 years ago by Jennifer Hillman Jackson25k

Thanks for your note...

The search interface is so much better here (not to mention other features) that I hope developers will switch here too.

I'll try posting here and summarizing on the list for developer questions.


ADD REPLYlink written 4.4 years ago by Brad Langhorst100
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