- galaxy-dev - lists.galaxyproject.org

New misc tool shed wish list
by Bjoern Gruening 27 Aug '13

27 Aug '13

Hi Greg, I tried to extend my old list [1] but I'm not allowed to edit it. Maybe you can add the following items to it. This time I collected a few items that are relevant for the Galaxy site of the Tool Shed ( When the user is installing via webinterface ) - offer an upgrade option, I think normally you are interested in new versions. At least an information about a new version should be displayed during the update. Or next to the revision number (e.g two new versions available) - distinguish more between update and upgrade - group different revisions of the same repository together - indicate if a revision is the latest revision available - a own category for workflows? Or the ability to tag a repository as workflow? - group the installed tools in categories Overall it looks really nice currently and I'm somehow enjoying installing and testing tools :) Thanks, Bjoern [1] https://trello.com/c/CIdMDeCd/988-toolshed-miscellaneous-issues-reported-by…

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Re: [galaxy-dev] Manhattan/qq plots
by Ross 27 Aug '13

27 Aug '13

Hi, Thomas. There are no resources available to support that now 3 year old rgenetics code so I'm sad but not surprised to hear of this new problem. The grant ended long ago and I no longer work with SNP so have no excuse to keep fixing or working on it. Is someone using this code willing to take it over, fix these kinds of bugs and add automated installation to bring it up to speed ? I'll help all I can but without a volunteer, the code should be considered deprecated and will soon disappear from the distribution. On Tue, Aug 27, 2013 at 2:14 AM, Bjoern Gruening <bjoern.gruening(a)gmail.com>wrote: > Hi Thomas, > > I think you are running a to new version of gplot > > http://blog.rstudio.org/2012/09/07/ggplot2-0-9-2/ > > opts is now deprecated and likely causes that error. Can you downgrade > the gplot version? > We are working on a R dependencies mechanism but we are not done yet, > sorry. > > Hope that helps, > Bjoern > > > 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 > > > > > > ___________________________________________________________ > > 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/ > > > > To search Galaxy mailing lists use the unified search at: > > http://galaxyproject.org/search/mailinglists/ > > > > ___________________________________________________________ > 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/ > > To search Galaxy mailing lists use the unified search at: > http://galaxyproject.org/search/mailinglists/ > -- Ross Lazarus MBBS MPH; Head, Medical Bioinformatics, BakerIDI; Tel: +61 385321444 http://scholar.google.com/citations?hl=en&user=UCUuEM4AAAAJ

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ncbi_blast_plus - tool shed updates
by Shantanu Pavgi (Campus) 27 Aug '13

27 Aug '13

I am trying to get repository updates for the ncbi_blast_plus tool which is making following request to the toolshed<http://toolshed.g2.bx.psu.edu/repository/check_for_updates?galaxy_url=http:…> site: http://toolshed.g2.bx.psu.edu/repository/check_for_updates?galaxy_url=http:… This request is coming back with following response with latest_changeset_revision same as changeset_revision. http://localhost:5000/admin_toolshed/update_to_changeset_revision?tool_shed… This results in following message in the browser: "The installed repository named 'ncbi_blast_plus' is current, there are no updates available.". The latest ncbi_blast_plus changeset revision in the toolshed is "9dabbfd73c8a", so I am not sure why above update request is coming back with d375502056f1 revision. Any clues on what might be wrong here? Appreciate any further debugging steps. -- Thanks, Shantanu

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Login hook
by Maddhi, Srinivas 26 Aug '13

26 Aug '13

Hello, Does Galaxy provide a post-login hook that could be used to trigger an operating system level action upon successful login ? Here is the scenario and use-case where that would come in handy: * Local instance of Galaxy (Nov 2012 release) on a Linux server with a PostgreSQL DB * Upload via FTP feature is enabled * Users are authenticated via LDAP and nginx * Users should be able to securely upload files (to their sub-directory within the configured FTP upload directory) The current method being employed to fulfill this use-case is through a modification to Š/galaxy-dist/lib/galaxy/web/framework/__init__.py file that calls a a shell script which creates an OS-level user and associated FTP upload directory. Files are uploaded by users via sFTP (SSHD configured to restrict Galaxy users to a chroot'ed directory). Options considered: * Shell/Python script that periodically queries the "galaxy_user" table and creates an OS-level user and FTP upload directory (not yet tried; introduces delay between user creation and FTP capability unless frequency of polling is high) * ProFTPD with sFTP and LDAP modules (increased administrative overhead compared to using built-in SSHD; wasn't able to get auto directory creation to work due to TBD cause) * PostgreSQL listen-notify to call a sFTP user creation script when an insert occurs in the "galaxy_user" table (not yet tried) Thank you. -- Senior Systems Administrator Iowa Institute for Human Genetics ITS Research Services, The University of Iowa

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TS API installation broken
by Bjoern Gruening 26 Aug '13

26 Aug '13

Hi, if I try to install a repository via API I get the following error: Traceback (most recent call last): File "/home/gruening/projects/code/galaxy-central/lib/galaxy/web/framework/__init__.py", line 189, in decorator rval = func( self, trans, *args, **kwargs) File "/home/gruening/projects/code/galaxy-central/lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py", line 265, in install_repository_revision tool_shed_repository_dict = tool_shed_repository.as_dict( value_mapper=default_tool_shed_repository_value_mapper( trans, tool_shed_repository ) ) File "/home/gruening/projects/code/galaxy-central/lib/galaxy/model/__init__.py", line 3350, in as_dict return self.dictify( view='element', value_mapper=value_mapper ) File "/home/gruening/projects/code/galaxy-central/lib/galaxy/model/__init__.py", line 3445, in dictify raise Exception( 'Unknown API view: %s' % view ) Exception: Unknown API view: element Command line: python ./scripts/api/install_tool_shed_repositories.py --api f1326e8588535c628f03a0df517e2247 -l http://localhost:8080 --url http://toolshed.g2.bx.psu.edu/ -o devteam -r 4676e145a44e --name add_value Cheers, Bjoern

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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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