August 2013 - galaxy-dev - lists.galaxyproject.org

manage toolshed repos crashing
by Robert Baertsch 26 Aug '13

26 Aug '13

When I click on manage installed tool shed repos on the admin screen, I get this error. Any ideas how to debug? -Robert ⇝ UnicodeDecodeError: 'ascii' codec can't decode byte 0xe2 in position 26: ordinal not in range(128) URL: http://su2c-dev.ucsc.edu/admin_toolshed/browse_repositories Module weberror.evalexception.middleware:364 in respond view >> app_iter = self.application(environ, detect_start_response) Module paste.recursive:84 in __call__ view >> return self.application(environ, start_response) Module paste.httpexceptions:633 in __call__ view >> return self.application(environ, start_response) Module galaxy.web.framework.base:132 in __call__ view >> return self.handle_request( environ, start_response ) Module galaxy.web.framework.base:190 in handle_request view >> body = method( trans, **kwargs ) Module galaxy.web.framework:221 in decorator view >> return func( self, trans, *args, **kwargs ) Module galaxy.webapps.galaxy.controllers.admin_toolshed:151 in browse_repositories view >> return self.installed_repository_grid( trans, **kwd ) Module galaxy.web.framework.helpers.grids:290 in __call__ view >> kwargs=kwargs ) Module galaxy.web.framework:991 in fill_template view >> return self.fill_template_mako( filename, **kwargs ) Module galaxy.web.framework:1006 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 _base_mako:42 in render_body view >> __M_writer(unicode(next.body())) Module _grid_base_mako:127 in render_body view >> __M_writer(unicode(self.grid_body( grid ))) Module _grid_base_mako:747 in render_grid_body view >> __M_writer(unicode(self.make_grid( grid ))) Module _grid_base_mako:777 in render_make_grid view >> __M_writer(unicode(self.render_grid_table( grid, show_item_checkboxes ))) Module _grid_base_mako:724 in render_render_grid_table view >> __M_writer(unicode(render_grid_table_body_contents( grid, show_item_checkboxes ))) Module _grid_base_mako:627 in render_grid_table_body_contents view >> return render_render_grid_table_body_contents(context,grid,show_item_checkboxes) Module _grid_base_mako:335 in render_render_grid_table_body_contents view >> value = column.get_value( trans, grid, item ) Module tool_shed.galaxy_install.grids.admin_toolshed_grids:61 in get_value view >> elif tool_shed_repository.missing_tool_dependencies: Module galaxy.model:3621 in missing_tool_dependencies view >> for tool_dependency in self.tool_dependencies: Module sqlalchemy.orm.attributes:168 in __get__ view Module sqlalchemy.orm.attributes:453 in get view Module sqlalchemy.orm.strategies:508 in _load_for_state view Module sqlalchemy.orm.strategies:574 in _emit_lazyload view Module sqlalchemy.orm.query:2115 in all view Module sqlalchemy.orm.query:2341 in instances view Module sqlalchemy.engine.base:3204 in fetchall view Module sqlalchemy.engine.base:3350 in _fetchall_impl view UnicodeDecodeError: 'ascii' codec can't decode byte 0xe2 in position 26: ordinal not in range(128)

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Why does my trackster complain about not being able to display BED files?
by Anthonius deBoer 26 Aug '13

26 Aug '13

Hi, I am using the latest version of galaxy at my local installation and I try to use trackster to display a simple BED file, but it invariably complains about not having a converter for this datatype and it tells me to check my datatypes_conf.xml which I did (not sure what I should be looking for, but this is the section on BED files... Am I missing a converter? And why would a BED file even needed to be converted? Thanks Thon <datatype extension="bed" type="galaxy.datatypes.interval:Bed" display_in_upload="true"> <converter file="bed_to_gff_converter.xml" target_datatype="gff"/> <converter file="interval_to_coverage.xml" target_datatype="coverage"/> <converter file="bed_to_bgzip_converter.xml" target_datatype="bgzip"/> <converter file="bed_to_tabix_converter.xml" target_datatype="tabix" depends_on="bgzip"/> <converter file="bed_to_summary_tree_converter.xml" target_datatype="summary_tree"/> <converter file="bed_to_fli_converter.xml" target_datatype="fli"/>   <display file="igb/bed.xml" /> </datatype> <datatype extension="bedgraph" type="galaxy.datatypes.interval:BedGraph" display_in_upload="true"> <converter file="bedgraph_to_bigwig_converter.xml" target_datatype="bigwig"/> </datatype> <datatype extension="bedstrict" type="galaxy.datatypes.interval:BedStrict" />  <datatype extension="bed12" type="galaxy.datatypes.interval:Bed12" /> <datatype extension="len" type="galaxy.datatypes.chrominfo:ChromInfo" display_in_upload="true"> <converter file="len_to_linecount.xml" target_datatype="linecount" /> </datatype> <datatype extension="bigbed" type="galaxy.datatypes.binary:BigBed" mimetype="application/octet-stream" dis

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Manhattan/qq plots
by Berner, Thomas 26 Aug '13

26 Aug '13

Hey guys, we are running a local galaxy instance (10200:fd4113962c32)with R version 3.0.1 and want to use Manhattan/qq, but we are missing the pval manhatan.pdf, only pval qqplot.pdf is generated and we are getting the following error: Nonzero exit code = 1 [1] "### 11008 values read from /opt/galaxy/galaxy-dist/database/files/002/dataset_2408.dat read - now running plots" 'opts' is deprecated. Use 'theme' instead. (Deprecated; last used in version 0.9.1) Setting the plot title with opts(title="...") is deprecated. Use labs(title="...") or ggtitle("...") instead. (Deprecated; last used in version 0.9.1) Scale for 'x' is already present. Adding another scale for 'x', which will replace the existing scale. Scale for 'y' is already present. Adding another scale for 'y', which will replace the existing scale. [1] "## qqplot on pval done" [1] "## manhattan on pval starting 1 2 3" Error in structure(list(call = match.call(), aesthetics = aesthetics, : argument "values" is missing, with no default Calls: rgqqMan ... scale_colour_manual -> manual_scale -> discrete_scale -> structure Execution halted At the galaxy-main ist working without any problems using the same input file. All the necessary packages should be installed. Any ideas? Thanks for your help. Thomas

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Galaxy in the cloud.... some questions
by Alistair Chilcott 23 Aug '13

23 Aug '13

Hi, Firstly this is my first post to the list so be gentle :D We have been looking at the Galaxy in the Cloud option for our researchers We have been doing a fair bit of reading on the various source but haven't found any solid answers to the following questions: -When it is started (AWS account setup and launched from the "new cloud cluster link") how much config is required to get it running all the tools such as megablast, Bowtie, Tophat etc? (We have also been setting up a local install of Galaxy but are struggling with the setup of these tools that don't come bundled with the base Galaxy install) -What size AWS cluster would be required to support a class of 20 or so students running a range of relatively short tasks with Megablast, Bowtie, Tophat, Fastq Groomer, SAM tools? -how is the AWS charge calculated does it run while the cluster is available or just for the actual compute time used? Ie Could setup it up and have it ready but while it isn't processing data it's not costing anything? Regards, Alistair [Description: Description: Description: Description: Description: Description: cid:image001.png@01CA36CF.30513900] Alistair Chilcott Systems Administrator, (Domain) Information Technology Services Email: alistair.chilcott(a)utas.edu.au<mailto:alistair.chilcott@utas.edu.au> | P: +61 3 6226 7743 University of Tasmania, Locked Bag 23, Hobart Tas. 7000

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Plugins
by Michael E. Cotterell 23 Aug '13

23 Aug '13

Are there any plans in the works to support plugins within Galaxy? One of the tools I'm working on is actually more of an extension of the workflow canvas/editor's user interface. Right now, I've minimized the modifications required to the editor.mako file to simply adding a mako include near the bottom of the file. However, like I just said, this requires editing a Galaxy file. It would be a lot better if Galaxy supported plugins with hooks, thus allowing me to extend the user interface (or any other part of the application) by registering hooks in a plugin. To demonstrate how easy it would be to integrate plugins into a python application, I've written up a simple plugin manager script (~100 loc) an placed it in a gist: https://gist.github.com/mepcotterell/6004997. Using this (or something similar to this) would make Galaxy extremely extensible. The only hard part would be figuring out where you want to place the hooks and documenting them for plugin developers. Sincerely, Michael E. Cotterell Ph.D. Student in Computer Science, University of Georgia Instructor of Record, Graduate RA & TA, University of Georgia Faculty Liaison, CS Graduate Student Association, University of Georgia mepcotterell(a)gmail.com (mailto:mepcotterell@gmail.com) mepcott(a)uga.edu (mailto:mepcott@uga.edu) mec(a)cs.uga.edu (mailto:mec@cs.uga.edu) http://michaelcotterell.com/

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How to send a file from galaxy to an external URL
by Delphine Lariviere 23 Aug '13

23 Aug '13

Dear Galaxy developers, I am a beginner in galaxy development and I need to build a tool to send a file from galaxy to an external URL. I tried to work with the following tutorial : http://wiki.galaxyproject.org/ **Admin/Tools/External%**20Display%20Applications%**20Tutorial<http://wiki.galaxyproject.org/Admin/Tools/External%20Display%20Applications…> But I couldn't make it work and it doesn't seem to fit exactly to what I want to do. I would be grateful if someone could help me with this issue, Thank you everyone, Delphine -- Delphine Larivière Ph.D Student in Bioinformatics CIRAD Data Integration Team email: delphine.lariviere(a)cirad.fr

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How to retrieve the current job ID
by Peng Li 22 Aug '13

22 Aug '13

Hi All I am working on one galaxy tool that could output results to database and I want to link the data records with galaxy job table by job id. Is it possible to retrieve the current job id in the tools config or tools code? I read the wikis and manuals and only find one Deprecated tag <code> has some clues like exec_after_job()? Does anyone know how to achieve this? Best regards -lee

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Stopping jobs by deleting history via API
by Sytchev, Ilya 22 Aug '13

22 Aug '13

Hi, I was wondering if there are any near term plans to fix this issue? https://trello.com/c/Tbota8xG/992-deleting-history-using-the-api-does-not-d elete-stop-jobs Thanks, Ilya

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developing a tool which could encapsulate any tool
by Ketan Maheshwari 22 Aug '13

22 Aug '13

Hi All, I am trying to develop a generic Galaxy tool which could encapsulate any other Galaxy tool and run it. The motivation behind this development is to enable running ordinary Galaxy tools in parallel with multiple datasets and/or running ordinary tools on large-scale compute resources. I was wondering about the Galaxy-way of doing this. Is there a natural pattern I could adapt here for this work? Are there any existing examples which does this? Thanks, -- Ketan

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Passing user_email to a data source
by Anthony Bretaudeau 22 Aug '13

22 Aug '13

Hello, I'm trying to add a new data source to my Galaxy instance, using synchronous data depositing. The data source needs to know the email address of the user who tries to import data to the Galaxy server. I would have like to write something like that: <inputs action="https://example.com/my/data/source" check_values="false" method="get"> <display>Browse the XX data source $GALAXY_URL</display> <param name="user_email" type="hidden" value="$__user_email__" /> </inputs> Then Galaxy would have generated this url: https://example.com/my/data/source?GALAXY_URL=http....&user_email=test@exam… But this doesn't work, because the $__user_email__ seems to be available only in <command> tag. I end up with this url which is useless: https://example.com/my/data/source?GALAXY_URL=http....&user_email=$__user_e… Is there any way to do what I need to do? It would be great if variables were available in <param> tags too. Otherwise, maybe I could write a custom tool type to do this. Is there any guideline for this? I have seen someone talking about that a few months ago, but with no answer: http://lists.bx.psu.edu/pipermail/galaxy-dev/2012-September/011258.html Thanks for your help Regards Anthony Bretaudeau

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