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

Job is waiting to run
by Fenglou Mao 11 Dec '12

11 Dec '12

I have a local galaxy server, and I built a workflow, it got stuck in one step in the middle. The computer is a 64 cores server, and no other jobs running in this server. Any idea how to trouble shooting? Thanks, Fenglou

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Installing Job Runners on a Cluster
by Ganote, Carrie L 11 Dec '12

11 Dec '12

Hi all, I could use some help getting DMRAA to run. We already have a galaxy instance with pbs running, but I'd like to connect to Torque using dmraa because we eventually intend to port over to a different resource manager. I've followed these instructions: http://apps.man.poznan.pl/trac/pbs-drmaa/wiki#Introduction http://wiki.galaxyproject.org/Admin/Config/Performance/Cluster Got dmraa installed and exported a path in my shell config: (PREFIX is long so I omitted it) DRMAA_LIBRARY_PATH=PREFIX/drmaa/lib/libdrmaa.so.1.0.12 in my universe_wsgi.ini: start_job_runners = drmaa default_cluster_job_runner = drmaa://-q tstgalxy -V/ addValue = drmaa:/// Here's my pbs_drmaa.conf: wait_thread: 0, pool_delay: 5, keep_completed: 60, user_state_dir: PREFIX/%s/jobs, I tried something simple like the add value tool. When I run it, I get the following error state: perl: warning: Setting locale failed. perl: warning: Please check that your locale settings: LANGUAGE = (unset), LC_ALL = (unset), LC_CTYPE = "en_US", LANG = "C" are supported and installed on your system. perl: warning: Falling back to the standard locale ("C"). The output file is actually correct, Galaxy just thinks there's an error. I get 2 files in user_state_dir with a job number and .started (empty) and .exitcode (0). Sounds like an env issue? If I run the perl script generated in the .sh file, it works fine. Output as expected. If I use local:/// it works fine with no error. I couldn't find any documentation on how to actually link dmraa to torque. Am I missing something major? Thanks in advance, Carrie Ganote

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Re-installing error persists
by Franco Caramia 11 Dec '12

11 Dec '12

Hi Greg, I have now modified the tool_dependencies.xml thank you for that.. I still have problems re-installing the tool... (need to reinstall to update the tool dependency and test it correctly) Is the reinstalling failure related to my galaxy version?? Here is the error: Server Error URL: http://bioinf-galaxy/admin_toolshed/browse_repositories?operation=activate+o r+reinstall&id=88ee2d7021e4dc1a Module paste.exceptions.errormiddleware:143 in __call__ >> <http://bioinf-galaxy:83/admin_toolshed/browse_repositories?operation=activa… r+reinstall&id=88ee2d7021e4dc1a#> app_iter = self.application(environ, start_response) Module paste.debug.prints:98 in __call__ >> <http://bioinf-galaxy:83/admin_toolshed/browse_repositories?operation=activa… r+reinstall&id=88ee2d7021e4dc1a#> environ, self.app) Module paste.wsgilib:539 in intercept_output >> <http://bioinf-galaxy:83/admin_toolshed/browse_repositories?operation=activa… r+reinstall&id=88ee2d7021e4dc1a#> app_iter = application(environ, replacement_start_response) Module paste.recursive:80 in __call__ >> <http://bioinf-galaxy:83/admin_toolshed/browse_repositories?operation=activa… r+reinstall&id=88ee2d7021e4dc1a#> return self.application(environ, start_response) Module paste.httpexceptions:632 in __call__ >> <http://bioinf-galaxy:83/admin_toolshed/browse_repositories?operation=activa… r+reinstall&id=88ee2d7021e4dc1a#> return self.application(environ, start_response) Module galaxy.web.framework.base:160 in __call__ >> <http://bioinf-galaxy:83/admin_toolshed/browse_repositories?operation=activa… r+reinstall&id=88ee2d7021e4dc1a#> body = method( trans, **kwargs ) Module galaxy.web.framework:184 in decorator >> <http://bioinf-galaxy:83/admin_toolshed/browse_repositories?operation=activa… r+reinstall&id=88ee2d7021e4dc1a#> return func( self, trans, *args, **kwargs ) Module galaxy.web.controllers.admin_toolshed:350 in browse_repositories >> <http://bioinf-galaxy:83/admin_toolshed/browse_repositories?operation=activa… r+reinstall&id=88ee2d7021e4dc1a#> return self.reselect_tool_panel_section( trans, **kwd ) Module galaxy.web.framework:184 in decorator >> <http://bioinf-galaxy:83/admin_toolshed/browse_repositories?operation=activa… r+reinstall&id=88ee2d7021e4dc1a#> return func( self, trans, *args, **kwargs ) Module galaxy.web.controllers.admin_toolshed:1352 in reselect_tool_panel_section >> <http://bioinf-galaxy:83/admin_toolshed/browse_repositories?operation=activa… r+reinstall&id=88ee2d7021e4dc1a#> status=status ) Module galaxy.web.framework:746 in fill_template >> <http://bioinf-galaxy:83/admin_toolshed/browse_repositories?operation=activa… r+reinstall&id=88ee2d7021e4dc1a#> return self.fill_template_mako( filename, **kwargs ) Module galaxy.web.framework:757 in fill_template_mako >> <http://bioinf-galaxy:83/admin_toolshed/browse_repositories?operation=activa… r+reinstall&id=88ee2d7021e4dc1a#> return template.render( **data ) Module mako.template:296 in render >> <http://bioinf-galaxy:83/admin_toolshed/browse_repositories?operation=activa… r+reinstall&id=88ee2d7021e4dc1a#> return runtime._render(self, self.callable_, args, data) Module mako.runtime:660 in _render >> <http://bioinf-galaxy:83/admin_toolshed/browse_repositories?operation=activa… r+reinstall&id=88ee2d7021e4dc1a#> **_kwargs_for_callable(callable_, data)) Module mako.runtime:692 in _render_context >> <http://bioinf-galaxy:83/admin_toolshed/browse_repositories?operation=activa… r+reinstall&id=88ee2d7021e4dc1a#> _exec_template(inherit, lclcontext, args=args, kwargs=kwargs) Module mako.runtime:718 in _exec_template >> <http://bioinf-galaxy:83/admin_toolshed/browse_repositories?operation=activa… r+reinstall&id=88ee2d7021e4dc1a#> callable_(context, *args, **kwargs) Module _base_mako:42 in render_body >> <http://bioinf-galaxy:83/admin_toolshed/browse_repositories?operation=activa… r+reinstall&id=88ee2d7021e4dc1a#> __M_writer(unicode(next.body())) Module _admin_tool_shed_repository_reselect_tool_panel_section_mako:76 in render_body >> <http://bioinf-galaxy:83/admin_toolshed/browse_repositories?operation=activa… r+reinstall&id=88ee2d7021e4dc1a#> __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 >> <http://bioinf-galaxy:83/admin_toolshed/browse_repositories?operation=activa… r+reinstall&id=88ee2d7021e4dc1a#> changeset_revision ) Module posixpath:67 in join >> <http://bioinf-galaxy:83/admin_toolshed/browse_repositories?operation=activa… r+reinstall&id=88ee2d7021e4dc1a#> elif path == '' or path.endswith('/'): AttributeError: 'NoneType' object has no attribute 'endswith' 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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Impersonate a User
by greg 11 Dec '12

11 Dec '12

Hi guys, I tried the impersonate a user feature, but I don't know how to stop impersonating a user? I tried going back to the impersonate a user feature and selecting myself but it's not clear if it changed anything, and I no longer see the History items I had before I did the impersonation. Thanks, Greg

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Mutation/SNP detection RNA-Seq
by suzan katie 11 Dec '12

11 Dec '12

Hi, I am trying to look mutations/SNPs in RNA-Seq data. Can anyone suggest me a workflow in Galaxy on how to detect SNPs and mutations Thanks in advance Suz

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problem with uploading data
by Banday, Abdul 11 Dec '12

11 Dec '12

Hi Nate, I loaded the file named s_6_1_sequence.txt.gz (Illumni file) under the login name abdul.banday(a)uconn.edu<mailto:abdul.banday@uconn.edu> as FTP.<ftp://ftp.R> Whenever I am trying to load it as history so that I can run it for analysis, the file upload is showing error and massage comes as data cannot be uncompressed. I have been trying to contact you guys from five days now. In one email you told me as soon as you have ftp transfer let me know. Could you check my file and see what is the problem. Thanking in anticipation. Postdoc at Uconn Rouf Banday

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Impossible to add a (new) tool in a workflow (in edition mode)
by Sarah Maman 11 Dec '12

11 Dec '12

Hello, For one of my tools that I have added to my local instance of Galaxy, I can not add this tool in the editing workflow. When I click on the tool name in the "tools" windows on the left, it does not appear in the editing workflow. Do you have any idea? Thank you in advance, Sarah Maman

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About the output
by Chenhao 11 Dec '12

11 Dec '12

I made a galaxy tool which is just create a txt file. When I use this tool , I wish to let it show the detail of the txt. In the xml file I use : <output> <data name="test" format="txt"><output/> But it does not work, when I click the "eye" button in galaxy, a download dialog appear, but it is just a empty file. Could somebody tell me what should I do , I want show the txt detail in the galaxy.

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Public Tool Shed Error
by Adam Carr (NBI) 11 Dec '12

11 Dec '12

Hi, I have been using the tool shed recently and come across a problem. When a searching for valid tools within the Public Tool Shed, it seems that if the search should return nothing found, it is instead displaying a Server Error page instead. For example: http://toolshed.g2.bx.psu.edu/repository/find_tools?tool_name=wibble Is currently returning an HTTP status code of 500 Internal Server Error. [cid:image001.png@01CDD78F.1E47CE90] --- Adam Carr Linux Support & Developmnent E adam.carr(a)nbi.ac.uk T +44 1603 450161 W jic.ac.uk ifr.ac.uk tgac.ac.uk tsl.ac.uk NBI Partnership Ltd Norwich Research Park Norwich NR4 7UH The NBI Partnership Ltd provides non-scientific services to the Institute of Food Research, the John Innes Centre, The Genome Analysis Centre and The Sainsbury Laboratory

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Displayed versions of tools in Galaxy
by Clare Sloggett 11 Dec '12

11 Dec '12

Hi guys, I wasn't sure if I should send this one to galaxy-user. I have just confused myself about the versions of tools displayed within Galaxy. If I select the TopHat tool, the tool UI says "Tophat for Illumina (version 1.5.0)". After I have run the job, the step panel in the History window says "Info: TopHat v1.4.1" If I select the Cufflinks tool, the tool UI says "Cufflinks (version 0.0.5)" After running the job, the step panel says "Info: cufflinks v1.3.0". Looking at the xml files, it does look like the version displayed before running is the wrapper and the version displayed on the resulting dataset is that of the command-line tool. <tool id="tophat" name="Tophat for Illumina" version="1.5.0">  <tool id="cufflinks" name="Cufflinks" version="0.0.5">  So looking at the XML it's very clear, but from the versions displayed in Galaxy I was completely confused, particularly since the two tophat version numbers happened to be similar (1.4.1 and 1.5.0). Maybe we should change it so that when Galaxy says "version" it is always explicit about whether it's "wrapper version" or just "version"? It also seems like there's no way for a user to discover the command-line tool version without actually running the tool (or is there)? Is this because Galaxy itself does not know this information? All this came about because I'm trying to specify to users which versions of tools my exported Workflow was built with, and I'm not sure how to do it without confusing them. Thanks, Clare -- Clare Sloggett Research Fellow / Bioinformatician Life Sciences Computation Centre Victorian Life Sciences Computation Initiative University of Melbourne, Parkville Campus 187 Grattan Street, Carlton, Melbourne Victoria 3010, Australia Ph: 03 903 53357 M: 0414 854 759

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