Re: [galaxy-dev] yaml import problem on startup
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 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 > 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 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) >>> >>> >>> ___ >>> Please keep all replies on the list by using "reply all" >>> in your mail client. To manage your subscriptions to this >>> and other Galaxy lists, please use the interface at: >>> https://lists.galaxyproject.org/ >>> >>> To search Galaxy mailing lists use the unified search at: >>> http://galaxyproject.org/search/mailinglists/ >>> >> >> > ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] yaml import problem on startup
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 mailto: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 mailto: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 mailto: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) ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] yaml import problem on startup
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 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 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) >> >> >> ___ >> Please keep all replies on the list by using "reply all" >> in your mail client. To manage your subscriptions to this >> and other Galaxy lists, please use the interface at: >> https://lists.galaxyproject.org/ >> >> To search Galaxy mailing lists use the unified search at: >> http://galaxyproject.org/search/mailinglists/ >> > > ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] yaml import problem on startup
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 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) > > > ___ > Please keep all replies on the list by using "reply all" > in your mail client. To manage your subscriptions to this > and other Galaxy lists, please use the interface at: > https://lists.galaxyproject.org/ > > To search Galaxy mailing lists use the unified search at: > http://galaxyproject.org/search/mailinglists/ > ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-dev] yaml import problem on startup
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) ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
