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.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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