On Jul 17, 2015 11:00 AM, galaxy-dev-request@lists.galaxyproject.org wrote:
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Today's Topics:
- Re: yaml import problem on startup (Marius van den Beek)
- Re: yaml import problem on startup (Marius van den Beek)
- Re: yaml import problem on startup (Poole, Richard)
- Re: Data Libraries: Unable to Link to Files When Paths Contain Spaces (John Chilton)
- Re: Error sorting or uploading Bam File (John Chilton)
- Re: CloudMan auto-scaling - Use spot instance for worker node? (Alexander Vowinkel)
- Re: Download data by data manager with non generic ftp-proxy (John Chilton)
- Re: CloudMan auto-scaling - Use spot instance for worker node? (Enis Afgan)
Message: 1 Date: Fri, 17 Jul 2015 12:23:06 +0200 From: Marius van den Beek m.vandenbeek@gmail.com To: "Poole, Richard" r.poole@ucl.ac.uk Cc: "galaxy-dev@lists.galaxyproject.org" galaxy-dev@lists.galaxyproject.org Subject: Re: [galaxy-dev] yaml import problem on startup Message-ID: < CACJqqiQo3uti7-doVVg_1L7-rzkwSxh9ccz2NSfJFUrg+kGsOQ@mail.gmail.com> Content-Type: text/plain; charset="utf-8"
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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