- galaxy-dev - lists.galaxyproject.org

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 02 Dec '12

02 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 02 Dec '12

02 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 02 Dec '12

02 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 02 Dec '12

02 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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Containing Multiple Datasets in a Single History Item
by Teddy Derego 30 Nov '12

30 Nov '12

Today we successfully set up the Barcode Splitter tool to send the outputs directly to the history, but the problem is that in some cases we want to use hundreds of bar codes, which would clutter the history. What I want to do is be able to output a text file containing the names of multiple datasets and have that sent to the history. Then, I want to create a workflow control that allows me to use that file to read multiple inputs into the workflow. So, I guess my real question is how would I create a new workflow control? Is it similar to creating a tool? Teddy

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Issue when enabling use_tasked_jobs with torque and nfs
by Carlos Borroto 30 Nov '12

30 Nov '12

Hi, In my environment when I activate 'use_tasked_jobs' I'm getting this message in "Info" with ncbi_blast wrappers: /local/opt/galaxy/galaxy-dist.8082/database/job_working_directory/000/9/task_0: Job output not returned from cluster Still the dataset with the blast result is green and contains the expected information. In the log I see: galaxy.jobs.runners.drmaa WARNING 2012-11-30 13:45:32,760 Job output not returned from cluster: [Errno 2] No such file or directory: '/local/opt/galaxy/galaxy-dist.8082/database/job_working_directory/000/9/task_0/9:1.drmout' And from torque I get this email: PBS Job Id: 1013.head Job Name: g9_toolshed_g2_bx_psu_edu_repos_devteam_ncbi_blast_plus_ncbi_blastn_wrapper_0_0_14_carlos_borroto_gmail_com Exec host: node01/0 An error has occurred processing your job, see below. Post job file processing error; job 1013.head on host node01/0 Unable to copy file /var/spool/torque/spool/1013.head.OU to galaxy@/local/opt/galaxy/galaxy-dist.8082/database/job_working_directory/000/9 /task_0/9:1.drmout *** error from copy cp: cannot create regular file `galaxy@/local/opt/galaxy/galaxy-dist.8082/database/job_working_directory/000/9/task_0/9:1.drmout': No such file or directory *** end error output Output retained on that host in: /var/spool/torque/undelivered/1013.head.OU Unable to copy file /var/spool/torque/spool/1013.head.ER to galaxy@/local/opt/galaxy/galaxy-dist.8082/database/job_working_directory/000/9 /task_0/9:1.drmerr *** error from copy cp: cannot create regular file `galaxy@/local/opt/galaxy/galaxy-dist.8082/database/job_working_directory/000/9/task_0/9:1.drmerr': No such file or directory *** end error output Output retained on that host in: /var/spool/torque/undelivered/1013.head.ER I think the problem is I'm forcing torque to use my nfs mounted shared file system: # cat /var/spool/torque/mom_priv/config $pbsserver head $usecp *:/home /home $usecp *:/local /local I can confirm this configuration is working fine with any other job not submitted through galaxy, both files are correctly copied to the working dir in that case. I'm using drmaa runner. I tried pbs, but in that case even without enabling tasked_jobs, while the err and out files are correctly copied and everything seems fine as far as I can tell, galaxy complains it can not find them. I tried increasing "retry_job_output_collection", but that didn't help. Cheers, Carlos

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