[galaxy-dev] Multiple .CEL file import for microarray analysis
Hi all, My apologies if this seems obvious to many of you (seems like something that will have been dealt with)- but I've been rooting around in the docs and mailing list to no concrete avail. I'm looking to Galaxyise our existing (somewhat informal) microarray analysis workflows. I've found rexpression etc and the associated helpful datatypes. But I'm stuck at the import of .CEL files: * Do I need to create a new datatype to represent .CEL? The fact this doesn't exist by default suggests it's not the right approach. * Assuming I was to do the above, how would I create a function to generate an affyBatch (for example) from an unspecified number of input .CEL? * Is the solution to have R work with a .tar and a config file to produce the affyBatch, thereby bypassing the .CEL requirement? But then there's no .tar datatype either. If I've missed the docs I'm happy to be chided and pushed in the right direction. Many 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: jmann...@staffmail.ed.ac.uk The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. ___ 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: http://lists.bx.psu.edu/
[galaxy-dev] Problem installing repositories from local tool shed: JSONDecodeError: No JSON object could be decoded: line 1 column 0 (char 0)
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=adb5f5c93f827949changeset_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: jmann...@staffmail.ed.ac.uk The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. ___ 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: http://lists.bx.psu.edu/
Re: [galaxy-dev] Problem installing repositories from local tool shed: JSONDecodeError: No JSON object could be decoded: line 1 column 0 (char 0)
Hi Greg, Thanks very much for the reply. I've actually just now worked around this- it was due somehow to our varnish/apache configs. I'll explain our setup and how I fixed this in case anyone else gets the same error. For context our setup is a number of virtual machines: * Varnish caching HTTP reverse proxy on one VM handles and caches requests, pointing them at one of a few apache instances running on a handful of other VMs. * A single mysql server itself running on a dedicated VM. * A high-memory multi-core VM we use for analysis purposes- which now also runs Galaxy. This machine also runs apache for various specialist reasons. I was sending things through varnish in order to use the cosign authentication we have set up there. I'm still doing that for toolshed administration purposes, but for the link from Galaxy itself for installing tools I've changed the line in tool_sheds_conf.xml to point directly at the apache on the Galaxy-running machine instead (which I configured appropriately to pass requests to the toolshed). That seems to have fixed things. Obviously this upsets the toolshed because it's not getting the user from Cosign, but I don't need galaxy to authenticate with the toolshed anyway, so I just set a dummy REMOTE_USER on the proxy request from the galaxy-local apache to keep the 'remote_user' setting in the toolshed config happy. Thanks again, Jon On 20/07/2012 15:57, Greg Von Kuster wrote: Hi Jon, It looks like your tool shed is not returning the information necessary for installing your tool shed repository into your local Galaxy instance. Try putting the following print statement just before line 978 in ~/lib/galaxy/web/controllers/admin_toolshed.py. This will tell you why the information is not json decodable. print raw_text: , raw_text It will be difficult for me to tell you what caused this since I do not have access to either your tool shed or your local Galaxy instance, so hopefully this will provide enough information for you to determine the cause. Thanks! Greg Von Kuster On Jul 20, 2012, at 8:51 AM, Jon Manning wrote: 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=adb5f5c93f827949changeset_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
