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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