Hi Marius,

I can also confirm that switching branches to revert the patch allows normal finishing of jobs. So its clearly related to the patches we applied yesterday to fix the metadata issue (see [galaxy-dev] Slow responses viewing histories).

However, I have noticed that even on an older non-patched branch of 15.05 I am still getting the same UserWarning about double yaml import upon Galaxy startup. So perhaps something about the metadata patches is somehow turning this warning into a tool fail?

Rich

On 17 Jul 2015, at 12:00, Marius van den Beek <m.vandenbeek@gmail.com> wrote:

Hi Richard,

Reverting the patch allows normal finishing of jobs, so unfortunately it seems 
we get a double import somewhere in the patch ... i'm suspecting it's 

from galaxy import app

in lib/galaxy/model/custom_types.py, but I don't know how to circumvent this.

Marius


On 17 July 2015 at 12:23, Marius van den Beek <m.vandenbeek@gmail.com> wrote:
Hi Richard, 

Well, I do have the same problem now (running bamtools), after applying the patch that should fix
metadata issue we discussed yesterday.
I'll dig into this.

Marius

On 17 July 2015 at 11:37, Poole, Richard <r.poole@ucl.ac.uk> wrote:
Hi all,

With the most recent update of Galaxy and also OS X 10.10.4 I am seeing this error message when first starting up the server:

/Users/galaxy/galaxy-dist/lib/galaxy/__init__.py:63: UserWarning: Module yaml was already imported from /Library/Python/2.7/site-packages/PyYAML-3.11-py2.7-macosx-10.10-intel.egg/yaml/__init__.pyc, but /Users/galaxy/galaxy-dist/eggs/PyYAML-3.10-py2.7-macosx-10.6-intel-ucs2.egg is being added to sys.path
  self.check_version_conflict()

This then is preventing certain tools from running correctly (such as samtools_filter (jjohnson) and they give the same error message when they fail:

/Users/galaxy/galaxy-dist/lib/galaxy/__init__.py:63: UserWarning: Module yaml was already imported from /Library/Python/2.7/site-packages/PyYAML-3.11-py2.7-macosx-10.10-intel.egg/yaml/__init__.pyc, but /Users/galaxy/galaxy-dist/eggs/PyYAML-3.10-py2.7-macosx-10.6-intel-ucs2.egg is being added to sys.path
  self.check_version_conflict()
Any thoughts?

Thanks,
Richard

Richard J Poole PhD
Wellcome Trust Fellow
Department of Cell and Developmental Biology
University College London
21 University Street, London WC1E 6DE
Office (518 Rockefeller): +44 20 7679 6577 (int. 46577)
Lab (529 Rockefeller): +44 20 7679 6133 (int. 46133)


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