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.po...@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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