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

Galaxy admin users
by 泽蔡 03 Dec '12

03 Dec '12

Hi all, I install a local instance on a linux system. And I tried to use the admin features of Galaxy, so I add my Galaxy login ( email ) to the list in the following config setting in the Galaxy configuration file universe_wsgi.ini. # this should be a comma-separated list of valid Galaxy users admin_users = xxxx@xxxx(the email I registered) But when I login, I did not see the "Admin" menu item on the top Galaxy menu bar. Why? Should I change anything esle?

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Galaxy & IGV display error
by PROTASIO＠clinic.ub.es 03 Dec '12

03 Dec '12

Hi all, I'm having problems when I click to visualize one BAM file from galaxy to IGV version 2.1.24. I've tried the local and also the web display options but I have the same problem. I have tried also to download first the bam file from galaxy and then loading into IGV manually and it works. I also have tried to modify the .jnlp generated but it does not work. IGV shows the next error message: ERROR [2012-11-26 11:44:54,591] [IGV.java:1555] [pool-1-thread-1] net.sf.samtools.util.RuntimeEOFException: Premature EOF; BinaryCodec in readmode; streamed file (filename not available) ERROR [2012-11-26 11:44:54,592] [IGV.java:1494] [pool-1-thread-1] Error loading tracks org.broad.igv.exceptions.DataLoadException: An error occurred while accessing: http://172.21.104.21:8080/display_application/9e23127bd2c9a880/igv_bam/web_…<br>Premature EOF; BinaryCodec in readmode; streamed file (filename not available) Thanks for your help. Joan Protasio, Bioinformatician & Software Engineer Bioinformatics Platform August Pi i Sunyer Biomedical Research Institute (IDIBAPS) C/ Rosselló 153, Barcelona http://bioinformatics.fcrb.es<http://bioinformatics.fcrb.es/> +34 93 227 54 00 ext. 4522

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The qiuck way to upload large file
by 泽蔡 03 Dec '12

03 Dec '12

Hi all, I'm a new guy of galaxy and bioinformatics. I read the document of galaxy, but it's so hard to find what I need. I already set up a locale instance of galaxy, it works fine. The problem is I need to analysis large data, but the "upload file" is so slow, is there some ways I can upload large file quickly?

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Activate or reinstall toolshed tool
by Franco Caramia 03 Dec '12

03 Dec '12

Hi devs, Sorry for the bad formating, here is the error I get when trying to reinstall a toolshed tool: Module paste.exceptions.errormiddleware:143 in __call__ >> app_iter = self.application(environ, start_response) Module paste.debug.prints:98 in __call__ >> environ, self.app) Module paste.wsgilib:539 in intercept_output >> app_iter = application(environ, replacement_start_response) Module paste.recursive:80 in __call__ >> return self.application(environ, start_response) Module paste.httpexceptions:632 in __call__ >> return self.application(environ, start_response) Module galaxy.web.framework.base:160 in __call__ >> body = method( trans, **kwargs ) Module galaxy.web.framework:184 in decorator >> return func( self, trans, *args, **kwargs ) Module galaxy.web.controllers.admin_toolshed:350 in browse_repositories >> return self.reselect_tool_panel_section( trans, **kwd ) Module galaxy.web.framework:184 in decorator >> return func( self, trans, *args, **kwargs ) Module galaxy.web.controllers.admin_toolshed:1352 in reselect_tool_panel_section >> status=status ) Module galaxy.web.framework:746 in fill_template >> return self.fill_template_mako( filename, **kwargs ) Module galaxy.web.framework:757 in fill_template_mako >> return template.render( **data ) Module mako.template:296 in render >> return runtime._render(self, self.callable_, args, data) Module mako.runtime:660 in _render >> **_kwargs_for_callable(callable_, data)) Module mako.runtime:692 in _render_context >> _exec_template(inherit, lclcontext, args=args, kwargs=kwargs) Module mako.runtime:718 in _exec_template >> callable_(context, *args, **kwargs) Module _base_mako:42 in render_body >> __M_writer(unicode(next.body())) Module _admin_tool_shed_repository_reselect_tool_panel_section_mako:76 in render_body >> __M_writer(unicode(render_tool_dependency_section( install_tool_dependencies_check_box, [ repo_info_dict ] ))) Module _admin_tool_shed_repository_common_mako:204 in render_render_tool_dependency_section >> changeset_revision ) Module posixpath:67 in join >> elif path == '' or path.endswith('/'): AttributeError: 'NoneType' object has no attribute 'endswith' Any ideas would be greatly appretiated. Also, if the galaxy devs have any (as a last resort) mysql script to delete a tool affecting all the pertinent tables it would great. Thanks, Franco This email (including any attachments or links) may contain confidential and/or legally privileged information and is intended only to be read or used by the addressee. If you are not the intended addressee, any use, distribution, disclosure or copying of this email is strictly prohibited. Confidentiality and legal privilege attached to this email (including any attachments) are not waived or lost by reason of its mistaken delivery to you. If you have received this email in error, please delete it and notify us immediately by telephone or email. Peter MacCallum Cancer Centre provides no guarantee that this transmission is free of virus or that it has not been intercepted or altered and will not be liable for any delay in its receipt.

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Reinstalling toolshed tool
by Franco Caramia 03 Dec '12

03 Dec '12

Hi devs, I get the following error when trying to reinstall a deleted repository/tool from the toolshed: Server Error URL: http://bioinf-galaxy/admin_toolshed/browse_repositories?operation=activate+o r+reinstall&id=88ee2d7021e4dc1a Module paste.exceptions.errormiddleware:143 in __call__ >> app_iter = self.application(environ, start_response) Module paste.debug.prints:98 in __call__ >> environ, self.app) Module paste.wsgilib:539 in intercept_output >> app_iter = application(environ, replacement_start_response) Module paste.recursive:80 in __call__ >> return self.application(environ, start_response) Module paste.httpexceptions:632 in __call__ >> return self.application(environ, start_response) Module galaxy.web.framework.base:160 in __call__ >> body = method( trans, **kwargs ) Module galaxy.web.framework:184 in decorator >> return func( self, trans, *args, **kwargs ) Module galaxy.web.controllers.admin_toolshed:350 in browse_repositories >> return self.reselect_tool_panel_section( trans, **kwd ) Module galaxy.web.framework:184 in decorator >> return func( self, trans, *args, **kwargs ) Module galaxy.web.controllers.admin_toolshed:1352 in reselect_tool_panel_section >> status=status ) Module galaxy.web.framework:746 in fill_template >> return self.fill_template_mako( filename, **kwargs ) Module galaxy.web.framework:757 in fill_template_mako >> return template.render( **data ) Module mako.template:296 in render >> return runtime._render(self, self.callable_, args, data) Module mako.runtime:660 in _render >> **_kwargs_for_callable(callable_, data)) Module mako.runtime:692 in _render_context >> _exec_template(inherit, lclcontext, args=args, kwargs=kwargs) Module mako.runtime:718 in _exec_template >> callable_(context, *args, **kwargs) Module _base_mako:42 in render_body >> __M_writer(unicode(next.body())) Module _admin_tool_shed_repository_reselect_tool_panel_section_mako:76 in render_body >> __M_writer(unicode(render_tool_dependency_section( install_tool_dependencies_check_box, [ repo_info_dict ] ))) Module _admin_tool_shed_repository_common_mako:204 in render_render_tool_dependency_section >> changeset_revision ) Module posixpath:67 in join >> elif path == '' or path.endswith('/'): AttributeError: 'NoneType' object has no attribute 'endswith' Any ideas?? Thanks, Franco This email (including any attachments or links) may contain confidential and/or legally privileged information and is intended only to be read or used by the addressee. If you are not the intended addressee, any use, distribution, disclosure or copying of this email is strictly prohibited. Confidentiality and legal privilege attached to this email (including any attachments) are not waived or lost by reason of its mistaken delivery to you. If you have received this email in error, please delete it and notify us immediately by telephone or email. Peter MacCallum Cancer Centre provides no guarantee that this transmission is free of virus or that it has not been intercepted or altered and will not be liable for any delay in its receipt.

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Installing dependencies
by Franco Caramia 03 Dec '12

03 Dec '12

Hi devs, Got the following error when trying to test the install of a dependency: URL: http://bioinf-galaxy/admin_toolshed/manage_tool_dependencies?sort=-create_ti me&show_item_checkboxes=false&async=false&page=1&webapp=galaxy&operation=ins tall&id=00f52b22f3524111& Module paste.exceptions.errormiddleware:143 in __call__ >> app_iter = self.application(environ, start_response) Module paste.debug.prints:98 in __call__ >> environ, self.app) Module paste.wsgilib:539 in intercept_output >> app_iter = application(environ, replacement_start_response) Module paste.recursive:80 in __call__ >> return self.application(environ, start_response) Module paste.httpexceptions:632 in __call__ >> return self.application(environ, start_response) Module galaxy.web.framework.base:160 in __call__ >> body = method( trans, **kwargs ) Module galaxy.web.framework:184 in decorator >> return func( self, trans, *args, **kwargs ) Module galaxy.web.controllers.admin_toolshed:904 in manage_tool_dependencies >> self.initiate_tool_dependency_installation( trans, tool_dependencies_for_installation ) Module galaxy.web.framework:184 in decorator >> return func( self, trans, *args, **kwargs ) Module galaxy.web.controllers.admin_toolshed:530 in initiate_tool_dependency_installation >> tool_dependencies_config = get_config_from_disk( 'tool_dependencies.xml', tool_shed_repository.repo_path( trans.app ) ) Module galaxy.util.shed_util:920 in get_config_from_disk >> for root, dirs, files in os.walk( relative_install_dir ): Module os:276 in walk >> names = listdir(top) TypeError: coercing to Unicode: need string or buffer, NoneType found Any ideas?? Thanks, Franco This email (including any attachments or links) may contain confidential and/or legally privileged information and is intended only to be read or used by the addressee. If you are not the intended addressee, any use, distribution, disclosure or copying of this email is strictly prohibited. Confidentiality and legal privilege attached to this email (including any attachments) are not waived or lost by reason of its mistaken delivery to you. If you have received this email in error, please delete it and notify us immediately by telephone or email. Peter MacCallum Cancer Centre provides no guarantee that this transmission is free of virus or that it has not been intercepted or altered and will not be liable for any delay in its receipt.

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status of deseq tool from main toolshed
by Ivan Lovric 03 Dec '12

03 Dec '12

Hi guys, Following the instructions in the README.md file from the successful installation of the tool, I copied deseq.R to tool-data/ I've been trying to get the deseq_and_sam2counts tool on our local galaxy-dist here: http://toolshed.g2.bx.psu.edu/repos/nikhil-joshi/deseq_and_sam2counts I note a prior message from Greg on certain <requirements> tags that should be added to get some things working in: http://dev.list.galaxyproject.org/environment-variables-and-paths-for-tools… It's probably not relevant to the error that I am getting at the moment since we've managed to install all those packages manually through R - source("http://bioconductor.org/biocLite.R") biocLite("DESeq") biocLite("aroma.light") The following dataset was used: dataset: 12345aba1345355777888aba24567888689 This is the error we get when running the tool. Note, it has executed the actual tool and made use of tool-data/deseq.R 29: Diagnostic Plots for DE Seq on data 27<https://galaxy-qld-dev.genome.edu.au/history> 0 bytes An error occurred running this job:*Error: Loading required package: Biobase Loading required package: BiocGenerics Loading required package: methods Attaching package: ‘BiocGenerics’ The following object(s) are masked from ‘package:stats’: xtabs The following object(s) are* * * * * Error: Loading required package: Biobase Loading required package: BiocGenerics Loading required package: methods Attaching package: ‘BiocGenerics’ The following object(s) are masked from ‘package:stats’: xtabs The following object(s) are masked from ‘package:base’: anyDuplicated, cbind, colnames, duplicated, eval, Filter, Find, get, intersect, lapply, Map, mapply, mget, order, paste, pmax, pmax.int, pmin, pmin.int, Position, rbind, Reduce, rep.int, rownames, sapply, setdiff, table, tapply, union, unique Welcome to Bioconductor Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, see 'citation("Biobase")', and for packages 'citation("pkgname")'. Loading required package: locfit locfit 1.5-8 2012-04-25 Loading required package: lattice Warning messages: 1: found methods to import for function ‘as.list’ but not the generic itself 2: found methods to import for function ‘eapply’ but not the generic itself Error in glm.fit(x = numeric(0), y = numeric(0), weights = NULL, start = c(0.1, : object 'fit' not found Calls: estimateDispersions ... parametricDispersionFit -> glm -> eval -> eval -> glm.fit In addition: Warning messages: 1: In is.na(rows) : is.na() applied to non-(list or vector) of type 'NULL' 2: In glm.fit(x = numeric(0), y = numeric(0), weights = NULL, start = c(0.1, : no observations informative at iteration 1 Any ideas?

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Data/history/user export and import
by Bossers, Alex 03 Dec '12

03 Dec '12

Dear all, Would it be possible somehow to not only export a single history of a user (to file) but also all histories of a user in one go. Or even all user-bound histories/settings and such? I would like to import them into another galaxy instance (basically from our internal development (galaxy_central) server to our public production (galaxy-dist) server), but going over them one-by-one will be a laborious task. Both instances are up-to-date. I do have admin access to both the galaxy instances (as we own them) so admin bound tools and/or possibilities from commandline would be suitable as well. Since I am unsure where it fits in the user-list or dev-list I cross-posted to both (sorry). Thanks in advance! Alex

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(no subject)
by Perez, Ricardo 02 Dec '12

02 Dec '12

Hi, We are having problems fetching sequences from our mysql database to galaxy. Does anyone know how to do so? Thank you for your help. --Ricardo Perez.

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hardware requirement for galaxy
by Huayan Gao 01 Dec '12

01 Dec '12

Hi there, I'm interested in the specifics of your Penn State setup. Can you send it to me? Thanks, Huayan

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