So it appears the error we encountered was because we just collected the
pull requests that concern the max_metada fix and applied them to the
release_15.05 of galaxy cloned from mercurial.

To resolve our problems we had to switch to git and then to checkout
release 15.05.
The below steps worked for Richard and me.

(~/galaxy-dist is my production galaxy dir):
cd ~
git clone https://github.com/galaxyproject/galaxy.git
cd galaxy
git reset --hard 3f1cec451f6dadee52a70a14fc6f6899f7aacdae
cd ~/galaxy-dist
hg update 17115
mv .hg .hg_backup
cp -R ~/galaxy/.git .
git pull #(at this point I got a merge error!)
#so I did:
git diff > local_changes.diff
cat local_changes.diff |patch -p1 -R
git pull
git checkout release_15.05

I do think that the metadata fixes should be pushed to mercurial quickly
though.

Marius

On 17 July 2015 at 13:00, Marius van den Beek <m.vandenb...@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.vandenb...@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.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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>>
>>
>
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