galaxy-dev August 2013

galaxy-dev@lists.galaxyproject.org

116 participants
210 discussions

job runner upload file
by Jasper Jan Koehorst 08 Aug '13

08 Aug '13

Hello, I have a very simple jobrunner script that allows only 1 job to be run as this galaxy is used for one thing in particular which consumes almost all resources. To do this I set the following: <plugins> <plugin id="local" type="runner" load="galaxy.jobs.runners.local:LocalJobRunner" workers="1"/> </plugins> This works, but is it possible to create a second worker that is only allowed to be used for uploading files? So people can upload their data already and only enter the queue for the big analysis? Otherwise if they turn their computer off in the evening the upload is gone...

2 1

ActionInputError undefined
by Jim Johnson 08 Aug '13

08 Aug '13

I was using the quotas api to update a quota amount and got the error: galaxy.web.framework ERROR 2013-07-30 15:40:59,149 Uncaught exception in exposed API method: Traceback (most recent call last): File "/Users/jj/gxt/gxt/lib/galaxy/web/framework/__init__.py", line 189, in decorator rval = func( self, trans, *args, **kwargs) File "/Users/jj/gxt/gxt/lib/galaxy/web/framework/__init__.py", line 221, in decorator return func( self, trans, *args, **kwargs ) File "/Users/jj/gxt/gxt/lib/galaxy/webapps/galaxy/api/quotas.py", line 108, in update except ActionInputError, e: NameError: global name 'ActionInputError' is not defined Was ActionInputError meant to be a class in lib/galaxy/exceptions/__init__.py ? diff -r 951e853b0bcd lib/galaxy/exceptions/__init__.py --- a/lib/galaxy/exceptions/__init__.py Tue Jul 30 12:54:02 2013 -0400 +++ b/lib/galaxy/exceptions/__init__.py Tue Jul 30 16:38:50 2013 -0500 @@ -21,6 +21,9 @@ class ItemOwnershipException( MessageException ): pass +class ActionInputError( MessageException ): + pass + class ObjectNotFound( Exception ): """ Accessed object was not found """ pass -- James E. Johnson, Minnesota Supercomputing Institute, University of Minnesota

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(no subject)
by Vipin TS 08 Aug '13

08 Aug '13

Hello dev-team, I have updated code repository of our production instance <https://galaxy.cbio.mskcc.org> to the recent galaxy-dist (10216:ebe87051fadf), now the instance page it is not rendering in a proper way. The error message I can see from the log file as follows: ------------------------------------------ x.x.x.x - - [08/Aug/2013:15:00:49 -0400] "GET / HTTP/1.1" 200 - "-" "Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/537.31 (KHTML, like Gecko) Chrome/26.0.1410.63 Safari/537.31" x.x.x.x - - [08/Aug/2013:15:00:50 -0400] "GET /root/tool_menu HTTP/1.1" 404 - "https://galaxy.cbio.mskcc.org/" "Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/537.31 (KHTML, like Gecko) Chrome/26.0.1410.63 Safari/537.31" x.x.x.x - - [08/Aug/2013:15:00:50 -0400] "GET /history HTTP/1.1" 200 - " https://galaxy.cbio.mskcc.org/" "Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/537.31 (KHTML, like Gecko) Chrome/26.0.1410.63 Safari/537.31" x.x.x.x - - [08/Aug/2013:15:00:50 -0400] "GET /history HTTP/1.1" 500 - " https://galaxy.cbio.mskcc.org/" "Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/537.31 (KHTML, like Gecko) Chrome/26.0.1410.63 Safari/537.31" ---------------------------------------- Exception happened during processing of request from ('127.0.0.1', 42042) Traceback (most recent call last): File "/codebase/eggs/Paste-1.7.5.1-py2.6.egg/paste/httpserver.py", line 1068, in process_request_in_thread self.finish_request(request, client_address) File "/usr/lib64/python2.6/SocketServer.py", line 322, in finish_request self.RequestHandlerClass(request, client_address, self) File "/usr/lib64/python2.6/SocketServer.py", line 617, in __init__ self.handle() File "/codebase/eggs/Paste-1.7.5.1-py2.6.egg/paste/httpserver.py", line 442, in handle BaseHTTPRequestHandler.handle(self) File "/usr/lib64/python2.6/BaseHTTPServer.py", line 329, in handle self.handle_one_request() File "/codebase/eggs/Paste-1.7.5.1-py2.6.egg/paste/httpserver.py", line 437, in handle_one_request self.wsgi_execute() File "/codebase/eggs/Paste-1.7.5.1-py2.6.egg/paste/httpserver.py", line 287, in wsgi_execute self.wsgi_start_response) File "/codebase/eggs/Paste-1.7.5.1-py2.6.egg/paste/urlmap.py", line 203, in __call__ return app(environ, start_response) File "/codebase/lib/galaxy/web/framework/middleware/request_id.py", line 12, in __call__ return self.app( environ, start_response ) File "/codebase/lib/galaxy/web/framework/middleware/xforwardedhost.py", line 21, in __call__ return self.app( environ, start_response ) File "/codebase/lib/galaxy/web/framework/middleware/translogger.py", line 68, in __call__ return self.application(environ, replacement_start_response) File "/codebase/lib/galaxy/web/framework/middleware/error.py", line 159, in __call__ exc_info) File "/codebase/lib/galaxy/web/framework/middleware/translogger.py", line 67, in replacement_start_response return start_response( status, headers, exc_info ) File "/codebase/lib/galaxy/web/framework/middleware/error.py", line 149, in __call__ app_iter = self.application(environ, sr_checker) File "/codebase/eggs/Paste-1.7.5.1-py2.6.egg/paste/recursive.py", line 84, in __call__ return self.application(environ, start_response) File "/codebase/eggs/Paste-1.7.5.1-py2.6.egg/paste/httpexceptions.py", line 633, in __call__ return self.application(environ, start_response) File "/codebase/lib/galaxy/web/framework/base.py", line 132, in __call__ return self.handle_request( environ, start_response ) File "/codebase/lib/galaxy/web/framework/base.py", line 199, in handle_request return body( environ, start_response ) File "/codebase/lib/galaxy/web/framework/__init__.py", line 985, in render template.render_context( context ) File "/codebase/eggs/Mako-0.4.1-py2.6.egg/mako/template.py", line 319, in render_context **kwargs) File "/codebase/eggs/Mako-0.4.1-py2.6.egg/mako/runtime.py", line 692, in _render_context _exec_template(inherit, lclcontext, args=args, kwargs=kwargs) File "/codebase/eggs/Mako-0.4.1-py2.6.egg/mako/runtime.py", line 718, in _exec_template callable_(context, *args, **kwargs) File "/codebase/database/compiled_templates/root/history.mako.py", line 73, in render_body if bool( [ data for data in history.active_datasets if data.state in ['running', 'queued', '', None ] ] ): AttributeError: 'Undefined' object has no attribute 'active_datasets' ---------------------------------------- Could you point me where I have to look to fix this issue. thanks in advance, --/Vipin

1 0

qa_url = slyfox?
by David Hoover 08 Aug '13

08 Aug '13

Strangely, I had never noticed this before. On some tools, there is a link at the top of the tool page that attempts to connect to http://slyfox.bx.psu.edu:8080/, which it can't. This URL is set via the qa_url directive in the universe_wsgi.ini file. What is this URL, and what should it be? David Hoover Helix Systems Staff

2 1

Galaxy on cluster with LSF scheduler
by Auerbach, Kenneth R. 08 Aug '13

08 Aug '13

Hello, Could anyone tell me if there are detailed instructions anywhere for setting up Galaxy on a Linux cluster using an LSF scheduler? Thank you. The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.

2 1

From workflow to script
by Victoria D Bohler 08 Aug '13

08 Aug '13

Hello, A naïve question, is it possible obtained from a galaxy-workflow a shell script?, if yes, how can I do it? Thank you in advance for your answer, Victoria

1 0

Galaxy with LSF scheduler
by Auerbach, Kenneth R. 08 Aug '13

08 Aug '13

Hello, Can anyone tell me if there are detailed instructions anywhere for setting up Galaxy on a Linux cluster using an LSF scheduler? Thank you. Ken. The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.

1 0

Oasesoptimiser Problem: Transcripts.fa not found
by Ricardo Perez 08 Aug '13

08 Aug '13

Dear all, When I try to run oasesoptimiser <https://galaxy.tamu.edu/tool_runner?tool_id=toolshed.g2.bx.psu.edu/repos/ko…> in Galaxy I get the following error: Traceback (most recent call last): File "/usr/local/galaxy/bioinfosoft/shed_tools/toolshed.g2.bx.psu.edu/repos/konradpaszkiewicz/oasesoptimiser/53e887dda799/oasesoptimiser/oases_optimiser.py", line 120, in <module> if __name__ == "__main__": __main__() File "/usr/local/galaxy/bioinfosoft/shed_tools/toolshed.g2.bx.psu.edu/repos/konradpaszkiewicz/oasesoptimiser/53e887dda799/oasesoptimiser/oases_optimiser.py", line 69, in __main__ for line in open(transcript_path): IOError: [Errno 2] No such file or directory: 'transcripts.fa' Anyone knows what is the source of this problem? Thank you for your time, --Ricardo Perez

1 0

Map with BWA results in correpted SAM file
by Moritz Juchler 08 Aug '13

08 Aug '13

Dear Galaxy Community, I have a local instance and installed 0.5.9-r16 BWA and the toolshed wrapper. The mapping is successful. I then use the Filter Sam Tool on the sam file from the alignment, but it spits out this error: *Dataset 26: Filter SAM on data 24* Tool execution generated the following error message: Traceback (most recent call last): File "/home/trr/galaxy-dist/tools/samtools/sam_bitwise_flag_filter.py", line 148, in <module> if __name__ == "__main__": main() File "/home/trr/galaxy-dist/tools/samtools/sam_bitwise_flag_filter.py", line 137, in main flags = int( fields[flag_col] ) ValueError: invalid literal for int() with base 10: 'RG:Z:lane712s006433' I have the same workflow online and did the exact same steps on the same fastq files. Is there anything I am missing? Is there any information I can provide to answer this question? Best Moritz

2 1

how to generate a workflow with customized tool names
by Jun Fan 08 Aug '13

08 Aug '13

Dear all, I have a tool which contains the function A,B, and C, the output of the function is the input of another function. I have developed a wrapper for this tool using conditional tag to allow users select the function they want. The label of the outputs (datasets) can be defined by label attribute in the outputs. So far so good. However, when I tried to create a workflow from history, the three steps (functions) from the tool are labeled with the same text (the title of the wrapper). My question is how to customize it, e.g. function_A_tool_name, function_B_tool_name which clearly tell the users which function is used instead of the need to check the parameter setting. Best regards! Dr Jun Fan Postdoctoral Researcher School of Biological and Chemical Sciences Queen Mary University of London

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galaxy-dev August 2013