- galaxy-dev - lists.galaxyproject.org

July 16, 2010 Galaxy Development News Brief
by Greg Von Kuster 16 Jul '10

16 Jul '10

The latest news brief is available at the following link. http://bitbucket.org/galaxy/galaxy-central/wiki/Features/DevNewsBrief/2010_… Greg Von Kuster Galaxy Development Team greg(a)bx.psu.edu

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upload files from filesystems path
by SHAUN WEBB 15 Jul '10

15 Jul '10

Hi, after updating to the latest galaxy changeset I am getting an error when trying to upload files from system path, the traceback is below. The new files then appear in the library as queued jobs. Thanks in advance for your help Shaun Webb URL: http://bifx3.bio.ed.ac.uk:8080/library_common/upload_library_dataset File '/opt/galaxy_dist/eggs/Paste-1.6-py2.5.egg/paste/exceptions/errormiddleware.py', line 143 in __call__ app_iter = self.application(environ, start_response) File '/opt/galaxy_dist/eggs/Paste-1.6-py2.5.egg/paste/debug/prints.py', line 98 in __call__ environ, self.app) File '/opt/galaxy_dist/eggs/Paste-1.6-py2.5.egg/paste/wsgilib.py', line 539 in intercept_output app_iter = application(environ, replacement_start_response) File '/opt/galaxy_dist/eggs/Paste-1.6-py2.5.egg/paste/recursive.py', line 80 in __call__ return self.application(environ, start_response) File '/opt/galaxy_dist/eggs/Paste-1.6-py2.5.egg/paste/httpexceptions.py', line 632 in __call__ return self.application(environ, start_response) File '/opt/galaxy_dist/lib/galaxy/web/framework/base.py', line 145 in __call__ body = method( trans, **kwargs ) File '/opt/galaxy_dist/lib/galaxy/web/controllers/library_common.py', line 978 in upload_library_dataset **kwd ) File '/opt/galaxy_dist/lib/galaxy/web/controllers/library_common.py', line 1158 in upload_dataset message=util.sanitize_text( message ), File '/opt/galaxy_dist/lib/galaxy/util/__init__.py', line 138 in sanitize_text for c in text: TypeError: 'NoneType' object is not iterable -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336.

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Possible Bug?
by Michael Siebauer 15 Jul '10

15 Jul '10

Hi, I maybe found a bug or misunderstand something in the debugging/logging section of universal_wsgi.ini I wanted to disable any logging and so commented everything within the logging section: |# ---- Logging and Debugging ------------------------------------------------ # Verbosity of log messages #log_level = DEBUG # Log memory usage #log_memory_usage = False # Log events #log_events = True # Log user actions #log_actions = False # Configuration for debugging middleware #debug = True #use_lint = False # Interactive debugging - NEVER enable this on a public site #use_interactive = False # Write thread status periodically to 'heartbeat.log' (careful, uses disk space rapidly!) #use_heartbeat = False # Enable the memory debugging interface (careful, negatively impacts server performance) #use_memdump = False # Profiling middleware (cProfile based) #use_profile = False | When I then start Galaxy the complete History shows only "Internal Server Error" and the Galaxy Log: |Starting server in PID 5470. serving on http://127.0.0.1:8080 192.168.3.90 - - [15/Jul/2010:17:29:23 +0200] "GET / HTTP/1.1" 200 - "-" "Mozilla/5.0 (X11; U; Linux x86_64; de; rv:1.9.0.19) Gecko/2010040121 Ubuntu/9.04 (jaunty) Firefox/3.0.19" 192.168.3.90 - - [15/Jul/2010:17:29:23 +0200] "GET /history HTTP/1.1" 200 - "http://bioapp07/" "Mozilla/5.0 (X11; U; Linux x86_64; de; rv:1.9.0.19) Gecko/2010040121 Ubuntu/9.04 (jaunty) Firefox/3.0.19" ---------------------------------------- Exception happened during processing of request from ('127.0.0.1', 38584) Traceback (most recent call last): File "/r1/people/galaxy/galaxy_dist/eggs/Paste-1.6-py2.6.egg/paste/httpserver.py", line 1053, in process_request_in_thread self.finish_request(request, client_address) File "/usr/lib/python2.6/SocketServer.py", line 320, in finish_request self.RequestHandlerClass(request, client_address, self) File "/usr/lib/python2.6/SocketServer.py", line 615, in __init__ self.handle() File "/r1/people/galaxy/galaxy_dist/eggs/Paste-1.6-py2.6.egg/paste/httpserver.py", line 432, in handle BaseHTTPRequestHandler.handle(self) File "/usr/lib/python2.6/BaseHTTPServer.py", line 329, in handle self.handle_one_request() File "/r1/people/galaxy/galaxy_dist/eggs/Paste-1.6-py2.6.egg/paste/httpserver.py", line 427, in handle_one_request self.wsgi_execute() File "/r1/people/galaxy/galaxy_dist/eggs/Paste-1.6-py2.6.egg/paste/httpserver.py", line 290, in wsgi_execute self.wsgi_write_chunk(chunk) File "/r1/people/galaxy/galaxy_dist/eggs/Paste-1.6-py2.6.egg/paste/httpserver.py", line 125, in wsgi_write_chunk "Content returned before start_response called") RuntimeError: Content returned before start_response called ---------------------------------------- 192.168.3.90 - - [15/Jul/2010:17:29:23 +0200] "GET /root/tool_menu HTTP/1.1" 200 - "http://bioapp07/" "Mozilla/5.0 (X11; U; Linux x86_64; de; rv:1.9.0.19) Gecko/2010040121 Ubuntu/9.04 (jaunty) Firefox/3.0.19" | After uncommenting everything in the logging section, galaxy works fine again. Whats the matter and how can I disable the debug messages, and especially: |192.168.3.90 - - [15/Jul/2010:17:29:23 +0200] "GET /root/tool_menu HTTP/1.1" 200 - "http://bioapp07/" "Mozilla/5.0 (X11; U; Linux x86_64; de; rv:1.9.0.19) Gecko/2010040121 Ubuntu/9.04 (jaunty) Firefox/3.0.19"| I use Galaxy behind a Apache with NIS userauthentification. Regards, Michael ;-)

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Error Uploading file
by Sébastien HARISPE 15 Jul '10

15 Jul '10

Hi, I encountered some difficulties to upload a file using tool interface. This returns the following error, see [1] .Upload a file using "Get data > Upload file" is not a problem. Xml tag used for tool definition : <param format="fasta" name="seq" type="file" label="Fasta file"/> Python version 2.6.5 (r265:79063) Do you know how this error can be solved? Sincerely, Seb [1] URL: http://127.0.0.1:8080/tool_runner/index File '/var/www/galaxy/galaxy_dist/eggs/WebError-0.8a-py2.6.egg/weberror/evalexception/middleware.py', line 364 in respond app_iter = self.application(environ, detect_start_response) File '/var/www/galaxy/galaxy_dist/eggs/Paste-1.6-py2.6.egg/paste/debug/prints.py', line 98 in __call__ environ, self.app) File '/var/www/galaxy/galaxy_dist/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/galaxy_dist/eggs/Paste-1.6-py2.6.egg/paste/recursive.py', line 80 in __call__ return self.application(environ, start_response) File '/var/www/galaxy/galaxy_dist/eggs/Paste-1.6-py2.6.egg/paste/httpexceptions.py', line 632 in __call__ return self.application(environ, start_response) File '/var/www/galaxy/galaxy_dist/lib/galaxy/web/framework/base.py', line 126 in __call__ body = method( trans, **kwargs ) File '/var/www/galaxy/galaxy_dist/lib/galaxy/web/controllers/tool_runner.py', line 68 in index template, vars = tool.handle_input( trans, params.__dict__ ) File '/var/www/galaxy/galaxy_dist/lib/galaxy/tools/__init__.py', line 837 in handle_input _, out_data = self.execute( trans, incoming=params ) File '/var/www/galaxy/galaxy_dist/lib/galaxy/tools/__init__.py', line 1109 in execute return self.tool_action.execute( self, trans, incoming=incoming, set_output_hid=set_output_hid ) File '/var/www/galaxy/galaxy_dist/lib/galaxy/tools/actions/__init__.py', line 327 in execute for name, value in tool.params_to_strings( incoming, trans.app ).iteritems(): File '/var/www/galaxy/galaxy_dist/lib/galaxy/tools/__init__.py', line 1112 in params_to_strings return params_to_strings( self.inputs, params, app ) File '/var/www/galaxy/galaxy_dist/lib/galaxy/tools/parameters/__init__.py', line 79 in params_to_strings value = params[ key ].value_to_basic( value, app ) File '/var/www/galaxy/galaxy_dist/lib/galaxy/tools/parameters/basic.py', line 103 in value_to_basic return self.to_string( value, app ) File '/var/www/galaxy/galaxy_dist/lib/galaxy/tools/parameters/basic.py', line 348 in to_string raise Exception( "FileToolParameter cannot be persisted" ) Exception: FileToolParameter cannot be persisted

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Collaborating on Galaxy - sharing and re-sharing histories
by Assaf Gordon 14 Jul '10

14 Jul '10

Hi all, I recently had to work closely with someone with our galaxy server, sharing histories back-and-forth with them. Each time they would run couple of jobs and share the history with me, and I'll check their results, perhaps run couple of jobs of my own and re-share the new results with them. The problem is that collaborating like that is quite annoying. Besides the need to go through so many clicks (of publish/share and list-histories-shared-with-me/clone/switch), another problem is that my histories list looks like this: === Clone of 'Clone of 'Clone of 'XXXX, BLAT' shared by 'gordon(a)cshl.edu' (active items only)' shared by 'xxxxxx(a)cshl.edu' (active items only)' shared by 'gordon(a)cshl.edu' (active items only) === Clone of 'Clone of 'xxxxxx, BLAT' shared by 'gordon(a)cshl.edu' (active items only)' shared by 'xxxxxxx(a)cshl.edu' (active items only) === Clone of 'xxxxxx, BLAT' shared by 'gordon(a)cshl.edu' (active items only) === and so on... each history adds just one or two more useful datasets, and it becomes cumbersome to manage all of them (not to mention that my histories-list and shared-histories-list are littered with the same history over and over). I think that in order to take galaxy to the 'next-level' of collaborative frame-work, a truly shared history mechanism will be useful: A single history instance, that once shared, every change made to it (by any user) will immediately appear on all users sharing this history. conceptually similar to http://piratepad.net/ (previously Etherpad), where all participants immediately see all the changes made to the content. Thanks, -gordon

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XML definition
by Sébastien HARISPE 14 Jul '10

14 Jul '10

Hi, I am trying to integrate some tools into Galaxy but I have encountered some difficulties in attempting to understand how the XML tool definition works exactly ... despite the XML tag documentation available at http://bitbucket.org/galaxy/galaxy-central/wiki/ToolConfigSyntax . Imagine a case where the presence of certain arguments depends on: - its value e.g we don't want to include it if its value is undefined - other arguments' values e.g if the value of x is greater than the y value we don't want to include the x argument on the command line How can I specify it using the XML definition? A simplified case: A tool needs arguments A and B or an input file F We want to propose two modes to configure it - [1] a basic mode where we can graphically set A and B values using fields such as text value... - [2] an advanced mode where we can specify a file containing complex configuration to upload tool command line: for [1] tool.py -A arg1 -B arg2 [2] tool.py -F confile I don't want to include the -F command line argument if -A and -B are defined I currently manage these cases using wrappers...quite boring Where can we find: - advanced documentation for XML definition - commented advanced examples - related discussions Best regards Seb [sorry for the bad english]

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Re: [galaxy-dev] [galaxy-user] microbes data in local instance of galaxy
by Daniel Blankenberg 13 Jul '10

13 Jul '10

Hi Alex, This data was obtained using scripts that are found under $GALAXY_ROOT/scripts/microbes/ and there is a README.txt file available here as well. However, it has been some time since these scripts have been used and it is possible that they have become stale and would require some tweaking to get working properly (IIRC there was some messy webpage scrapping involved). Thanks for using Galaxy, Dan On Jul 13, 2010, at 2:30 AM, Bossers, Alex wrote: > Hi All, > We have or local galaxy instance running which works fine. > In the get data section the Microbes tool has no local ncbi data. The public instance has it. > What is the best/easiest way to get that data into our local instance of galaxy. Have been browsing the wikis and looked through library and dataset documentations but was unable to resolve this at first glance. > Any help/guidance appreciated. > Thanks > Alex > _______________________________________________ > galaxy-user mailing list > galaxy-user(a)lists.bx.psu.edu > http://lists.bx.psu.edu/listinfo/galaxy-user

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Workflow copy history item
by Dennis Gascoigne 13 Jul '10

13 Jul '10

The copy history item is available from the Edit Attributes page for a history item. It would be more useful and a bit more logical if this option was available from the history drop down menu on the right and the history menu in the saved histories page. The reason/advantage to this is; * The history item copy page offers the capacity to copy one or more items from the history, it is not limited to the history item you click to the page from * It is much easier to * copy items between histories by selecting the option from the history menu, or from the history menus in the saved histories page, VS * opening a history, clicking on an edit attribute, scroll to the bottom of the page, click copy history item My apologies if this seems picky but I do this a lot. Cheers Dennis

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History link in main menu
by Dennis Gascoigne 13 Jul '10

13 Jul '10

This might seem minor, but a link to History manager in the main menu at the top (between Analyze and Workflow) would be really handy. It is much more common a destination than workflows but is an extra click/select away through the workflow menu on the right. A couple of users in our group have bought this up, and I kind of agree. Cheers Dennis

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Workflow Error
by Sumedha Ganjoo 12 Jul '10

12 Jul '10

Hi, I am using a tool that interacts with Web services via Galaxy. Run on its own in the Galaxy GUI, it works fine. But when we run it in a workflow, with other tools it sometimes runs correctly , sometimes gives the following error: OperationalError: (OperationalError) database is locked u'UPDATE job SET update_time=?, command_line=? WHERE job.id = ?' ['2010-07-12 14:10:18.398960', 'python ${installationDirectory}/tools/${............ ..................................................... I was wondering if Galaxy has some timeouts implemented in their workflows because of which if the first step takes a while the second step of the workflow is executed simultaneously? Or any other explanation for such behavior. I would really appreciate a reply as soon as possible. Thanks. Regards, Sumedha -- Sumedha Ganjoo Graduate Assistant, Department Of Computer Science, University Of Georgia, Athens, GA , USA

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