June 2012 - galaxy-dev - lists.galaxyproject.org

wrapping qvalue in Galaxy
by Christophe Antoniewski 06 Jun '12

06 Jun '12

Hi, I am trying to wrap the qvalue R package in a script (as I have already done for a dozen), but this time I have repeatedly the same error "*In fun(libname, pkgname) : no DISPLAY variable so Tk is not available*" or "*Loading Tcl/Tk interface ... done*" (and red, desperately red box). I already had this type of bugs and fixed them by using the suppressWarnings or suppressMessages R methods. But this time, no way. I really don't need the Tcl/Tk interface and I am not using it with qvalue... frustrating. (my code run into R in command lines like a charm) Any clue to shut off Galaxy and get this miserable pvalue vector output ? Christophe PS. I browsed the net, found traces of problems similar to mine, but unfortunately no trace of solutions.

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Galaxy edit page content bugs
by Felix Homa 06 Jun '12

06 Jun '12

Using the cookie_path setting makes user lose his session when editing pages. For some reason, if you activate the cookie_path setting in universe_wsgi.ini, the simple fact of opening the page editor (via the /page/edit_content URL) adds a new record to the galaxy_session database table, with a null user id. Therefore the previous valid session is lost and the user is asked to login again, no matter what his next action is. Someone can give me some help to resolve the problem, please ? Felix.

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Meme gives me UnicodeDecodeError. Is this an error from parsing the OUTPUT?
by Anthonius deBoer 05 Jun '12

05 Jun '12

Hi, I am trying to run MEME and I got this error below when running it. Is this an error complaining about the non-ASCII nature of the OUTPUT or of the program (or input?). Thanks Thon Error Traceback: View as: Interactive | Text | XML (full) ⇝ UnicodeDecodeError: 'ascii' codec can't decode byte 0xe2 in position 25: ordinal not in range(128) URL: http://srp106:8080/dataset/errors?id=176856 Module weberror.evalexception.middleware:364 in respond view >> app_iter = self.application(environ, detect_start_response) Module paste.debug.prints:98 in __call__ view >> environ, self.app) Module paste.wsgilib:539 in intercept_output view >> app_iter = application(environ, replacement_start_response) Module paste.recursive:80 in __call__ view >> return self.application(environ, start_response) Module paste.httpexceptions:632 in __call__ view >> return self.application(environ, start_response) Module galaxy.web.framework.base:160 in __call__ view >> body = method( trans, **kwargs ) Module galaxy.web.controllers.dataset:160 in errors view >> return trans.fill_template( "dataset/errors.mako", hda=hda ) Module galaxy.web.framework:733 in fill_template view >> return self.fill_template_mako( filename, **kwargs ) Module galaxy.web.framework:744 in fill_template_mako view >> return template.render( **data ) Module mako.template:296 in render view >> return runtime._render(self, self.callable_, args, data) Module mako.runtime:660 in _render view >> **_kwargs_for_callable(callable_, data)) Module mako.runtime:692 in _render_context view >> _exec_template(inherit, lclcontext, args=args, kwargs=kwargs) Module mako.runtime:718 in _exec_template view >> callable_(context, *args, **kwargs) Module dataset_errors_mako:74 in render_body view >> __M_writer(filters.html_escape(unicode(job.stdout ))) UnicodeDecodeError: 'ascii' codec can't decode byte 0xe2 in position 25: ordinal not in range(128)

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disk space for local galaxy
by Xu, Jianpeng 05 Jun '12

05 Jun '12

Hi, I have installed the local galaxy. I deleted a few histories in order to get some disk space. However, the disk space did not change after the deletion of the histories. Do you why ? How can I get some disk space by deleting histories ? Thanks, ________________________________ This e-mail message (including any attachments) is for the sole use of the intended recipient(s) and may contain confidential and privileged information. If the reader of this message is not the intended recipient, you are hereby notified that any dissemination, distribution or copying of this message (including any attachments) is strictly prohibited. If you have received this message in error, please contact the sender by reply e-mail message and destroy all copies of the original message (including attachments).

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pbs_submit failed, error 15035, Unknown resource
by Schwartz, Terri 04 Jun '12

04 Jun '12

Hi, When I try to use pbs job runners on my local galaxy installation I get an error message such as: galaxy.jobs.runners.pbs DEBUG 2012-06-04 12:57:02,827 (22) pbs_submit failed, PBS error 15035: Unknown resource I'm hoping someone can give me pointers about how to debug this or where to look for more debugging information. Thanks, Terri

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Tool migration error
by Shantanu Pavgi 04 Jun '12

04 Jun '12

I am trying to migrate EMBOSS tools from core galaxy code dir to shed_tools directory. I am getting following error with the migration script: {{{ sh ./scripts/migrate_tools/0002_tools.sh Traceback (most recent call last): File "./scripts/migrate_tools/migrate_tools.py", line 21, in <module> app = MigrateToolsApplication( sys.argv[ 1 ] ) File "/home/pavgi/galaxy-exp/lib/galaxy/tool_shed/migrate/common.py", line 81, in __init__ object_store=self.object_store ) File "/home/pavgi/galaxy-exp/lib/galaxy/model/mapping.py", line 1836, in init load_egg_for_url( url ) File "/home/pavgi/galaxy-exp/lib/galaxy/model/mapping.py", line 1816, in load_egg_for_url dialect = guess_dialect_for_url( url ) File "/home/pavgi/galaxy-exp/lib/galaxy/model/mapping.py", line 1812, in guess_dialect_for_url return (url.split(':', 1))[0] AttributeError: 'bool' object has no attribute 'split' }}} Following are tool shed related config files: {{{ $ cat tool_sheds_conf.xml <?xml version="1.0"?> <tool_sheds> <tool_shed name="Galaxy main tool shed" url="http://toolshed.g2.bx.psu.edu/"/> <tool_shed name="Galaxy test tool shed" url="http://testtoolshed.g2.bx.psu.edu/"/> </tool_sheds> $ cat shed_tool_conf.xml <?xml version="1.0"?> <toolbox tool_path="../shed_tools"> </toolbox> }}} I am using system Python 2.6 on CentOS 6.2 system. However, I was able to reproduce this error on CentOS 5.8 system with custom Python 2.6 install as well. Any pointers on what might be wrong here will be really helpful. -- Thanks, Shantanu

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GCC2012 Early Registration ends in 1 week
by Dave Clements 04 Jun '12

04 Jun '12

Hello all, Just a reminder that early registration for the 2012 Galaxy Community Conference (GCC2012) <http://galaxyproject.org/wiki/Events/GCC2012>, being held in Chicago, Illinois, July 25-27, *closes on June 11, one week from today*. Registering early saves 36 to 42% on registration costs, and allows you to book discounted conference lodging<http://wiki.g2.bx.psu.edu/Events/GCC2012/Logistics#Lodging> *before it fills up*. Register now<http://wiki.g2.bx.psu.edu/Events/GCC2012/Register> . GCC2012 <http://galaxyproject.org/wiki/Events/GCC2012> is about integrating, analyzing, and sharing the diverse and very large datasets that are now typical in biomedical research. This is an opportunity to share best practices with, and learn from, a large community of researchers and support staff who are facing the challenges of data-intensive biology. Galaxy <http://gmod.org/wiki/Galaxy> is an open web-based platform for data intensive biomedical research <http://galaxyproject.org> that is widely used and deployed at research organizations of all sizes and around the world. The GCC2012 Training Day<http://galaxyproject.org/wiki/Events/GCC2012/TrainingDay>agenda has been finalized. It has 3 parallel tracks, each featuring four, 90 minute workshops and covering 10 different topics. The final schedule<http://wiki.g2.bx.psu.edu/Events/GCC2012/Program>of speakers<http://wiki.g2.bx.psu.edu/Events/GCC2012/Program#Confirmed_Speakers>and abstracts <http://wiki.g2.bx.psu.edu/Events/GCC2012/Abstracts> are also now available. Hope to see you in Chicago! Dave Clements, on behalf of the GCC2012 Organizing Committee<http://galaxyproject.org/wiki/Events/GCC2012/Organizing%20Committee> -- http://galaxyproject.org/GCC2012 <http://galaxyproject.org/wiki/GCC2012> http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ http://galaxyproject.org/wiki/

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Tool Shed / Fabric upcoming integration
by Sebastian J Schultheiss 04 Jun '12

04 Jun '12

Dear Greg, according to the Tool Shed wiki page, you will be enabling installation of Tool Shed tools with 3rd party dependencies very soon. Together with Enis Afgan I created several fabric scripts a while ago that install some of our tools into an EC2 instance of Galaxy. We are now in the process of updating these scripts and wanted to add new ones. Is there already a (preliminary) framework that those fabric scripts should follow if they are to be packaged in the tool shed repository? Thanks for your help! -- Sebastian

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Issue with data
by Richard Linchangco 04 Jun '12

04 Jun '12

Dear Galaxy, I'm working with a data set with 8 samples and have run them through bow tie (previously) and am trying to run them in cufflinks now. The odd numbered samples I have run fine and produce data but the even numbered samples I have all produce no data in terms of an FPKM or any other calculation. I'm looking at gene expression and my test samples are in fact the even numbered ones that are not providing me with calculations. Is there a simple reason for this? Apologies if this is a simple question but I have tried to adjust the settings a few time to no avail. Any and all help would be greatly appreciated. Thanks! Sincerely, Richard Linchangco Richard Linchangco PSM in Bioinformatics College of Computing and Informatics University of North Carolina at Charlotte Tel: (630)440-7010 rlinchan(a)uncc.edu, rlinch2(a)gmail.com

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Re: [galaxy-dev] [galaxy-user] email database
by Hans-Rudolf Hotz 04 Jun '12

04 Jun '12

Hi Roger Have a look at the "Reserved Variables" on this wiki page: http://wiki.g2.bx.psu.edu/Admin/Tools/Tool%20Config%20Syntax?#A.3Ccommand.3… I guess, his is what you are after? Also, please use the 'galaxy-dev' mailing list (cc'ed) for questions regarding local installation, configuration, tool integration help, etc regards, Hans On 06/04/2012 11:54 AM, Roger Liu wrote: > hi im the new user at intalling my own galaxy > and i developing some of the tools > now i face a challenge > i need to call the login(now) email address form my tools > but i didnt find any API can did this > so i was wondering is there had any database store the email address > i need to identify the login user's email and return back to my tool > thanks > > > ___________________________________________________________ > The Galaxy User list should be used for the discussion of > Galaxy analysis and other features on the public server > at usegalaxy.org. Please keep all replies on the list by > using "reply all" in your mail client. For discussion of > local Galaxy instances and the Galaxy source code, please > use the Galaxy Development list: > > http://lists.bx.psu.edu/listinfo/galaxy-dev > > To manage your subscriptions to this and other Galaxy lists, > please use the interface at: > > http://lists.bx.psu.edu/

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