Hi all,
I'm new to Galaxy- so hello, and excuse me while I get to grips with all the conventions!
I've successfully got my local Galaxy (galaxy-central) install set up and working correctly, as well as a local toolshed. I've also linked the two with a line in tool_sheds_conf.xml. But I'm getting the following problem when I try to install tools from the local toolshed (either ones I tried to make myself, or ones I downloaded from the Galaxy public toolshed).
The following appears when I click 'install to local Galaxy':
URL: http://www.my.domain/galaxy/admin_toolshed/prepare_for_install?tool_shed_url=http://www.my.domain/toolshed/&repository_ids=adb5f5c93f827949&changeset_revisions=f5ee1108336b
File '/var/www/galaxy_home/galaxy-central/eggs/Paste-1.6-py2.6.egg/paste/exceptions/errormiddleware.py', line 143 in __call__
app_iter = self.application(environ, start_response)
File '/var/www/galaxy_home/galaxy-central/eggs/Paste-1.6-py2.6.egg/paste/debug/prints.py', line 98 in __call__
environ, self.app)
File '/var/www/galaxy_home/galaxy-central/eggs/Paste-1.6-py2.6.egg/paste/wsgilib.py', line 539 in intercept_output
app_iter = application(environ, replacement_start_response)
File '/var/www/galaxy_home/galaxy-central/eggs/Paste-1.6-py2.6.egg/paste/recursive.py', line 80 in __call__
return self.application(environ, start_response)
File '/var/www/galaxy_home/galaxy-central/lib/galaxy/web/framework/middleware/remoteuser.py', line 91 in __call__
return self.app( environ, start_response )
File '/var/www/galaxy_home/galaxy-central/eggs/Paste-1.6-py2.6.egg/paste/httpexceptions.py', line 632 in __call__
return self.application(environ, start_response)
File '/var/www/galaxy_home/galaxy-central/lib/galaxy/web/framework/base.py', line 160 in __call__
body = method( trans, **kwargs )
File '/var/www/galaxy_home/galaxy-central/lib/galaxy/web/framework/__init__.py', line 184 in decorator
return func( self, trans, *args, **kwargs )
File '/var/www/galaxy_home/galaxy-central/lib/galaxy/web/controllers/admin_toolshed.py', line 978 in prepare_for_install
repo_information_dict = from_json_string( raw_text )
File '/var/www/galaxy_home/galaxy-central/eggs/simplejson-2.1.1-py2.6-linux-x86_64-ucs4.egg/simplejson/__init__.py', line 384 in loads
File '/var/www/galaxy_home/galaxy-central/eggs/simplejson-2.1.1-py2.6-linux-x86_64-ucs4.egg/simplejson/decoder.py', line 402 in decode
File '/var/www/galaxy_home/galaxy-central/eggs/simplejson-2.1.1-py2.6-linux-x86_64-ucs4.egg/simplejson/decoder.py', line 420 in raw_decode
JSONDecodeError: No JSON object could be decoded: line 1 column 0 (char 0)
The following error sometimes (not always, but that may be due to my use of Varnish) pops up in my apache logs when the above appears, could this be linked?
File does not exist: /var/www/galaxy_home/galaxy-central/static/scripts/packed/modernizr.js, referer: http://www.my.domain/galaxy/admin
Pertinent configuration details:
* Galaxy and the toolshed proxied from Apache on another machine.
* A Cosign-based authentication system is in place, so 'use_remote_user = True' in both Galaxy and the toolshed.
* Galaxy's home dir is at /var/www/galaxy_home for consistency with other things I run.
All input appreciated.
Thanks,
Jon
--
Dr Jonathan Manning
Bioinformatics Team
Centre for Cardiovascular Science
University of Edinburgh
Queens Medical Research Institute
47 Little France Crescent
Edinburgh EH16 4TJ
United Kingdom
T: +44 131 242 6700
F: +44 131 242 6782
E: jmanning@staffmail.ed.ac.uk
The University of Edinburgh is a charitable body, registered in
Scotland, with registration number SC005336.
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