- galaxy-dev - lists.galaxyproject.org

error despite success
by Matthias Bernt 18 Oct '17

18 Oct '17

Dear list, today I got an erroneous result (red) despite the output of the tool to be seems fine. Seemingly there was an error during setting the metadata. ``` Fatal error: An error occured during execution, see stderr and stdout for more information Reading reference gene model /gpfs1/data/galaxy_server/galaxy-dev/database/files/002/dataset_2992.dat ... Done Loading SAM/BAM file ... Finished Total 62188 usable reads were sampled Traceback (most recent call last): File "/gpfs1/data/galaxy_server/galaxy-dev/jobs_dir/001/1858/set_metadata_Ad6q_v.py", line 1, in from galaxy_ext.metadata.set_metadata import set_metadata; set_metadata() File "/gpfs1/data/galaxy_server/galaxy-dev/lib/galaxy_ext/metadata/set_metadata.py", line 85, in set_metadata datatypes_registry.load_datatypes(root_dir=galaxy_root, config=datatypes_config) File "/gpfs1/data/galaxy_server/galaxy-dev/lib/galaxy/datatypes/registry.py", line 109, in load_datatypes tree = galaxy.util.parse_xml(config) File "/gpfs1/data/galaxy_server/galaxy-dev/lib/galaxy/util/__init__.py", line 214, in parse_xml root = tree.parse(fname, parser=ElementTree.XMLParser(target=DoctypeSafeCallbackTarget())) File "/global/apps/bioinf/galaxy/bin/Python-2.7.13/lib/python2.7/xml/etree/ElementTree.py", line 647, in parse source = open(source, "rb") IOError: [Errno 2] No such file or directory: '/gpfs1/data/galaxy_server/galaxy-dev/database/tmp/tmp_uHZbW' ``` Are there any suggestions how to continue with such a behavior. The file system on our cluster seems to be slow at the moment, could this be the cause? Best, Matthias -- ------------------------------------------- Matthias Bernt Bioinformatics Service Molekulare Systembiologie (MOLSYB) Helmholtz-Zentrum für Umweltforschung GmbH - UFZ/ Helmholtz Centre for Environmental Research GmbH - UFZ Permoserstraße 15, 04318 Leipzig, Germany Phone +49 341 235 482296, m.bernt(a)ufz.de, www.ufz.de Sitz der Gesellschaft/Registered Office: Leipzig Registergericht/Registration Office: Amtsgericht Leipzig Handelsregister Nr./Trade Register Nr.: B 4703 Vorsitzender des Aufsichtsrats/Chairman of the Supervisory Board: MinDirig Wilfried Kraus Wissenschaftlicher Geschäftsführer/Scientific Managing Director: Prof. Dr. Dr. h.c. Georg Teutsch Administrative Geschäftsführerin/ Administrative Managing Director: Prof. Dr. Heike Graßmann -------------------------------------------

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Problems with BlastDB.loc
by Enders Matthias 18 Oct '17

18 Oct '17

Dear Galaxy Dev List, we currently facing a problem with integrating new Blast Databases in our Galaxy instance. We added a the new DB to the file: /galaxy-central/tool-data/blastdb.loc But the new Database didn't show up in the respective tools, this situation remains also after restarting the galaxy instance and reloading the tool config (blasn for example). As we included several databases before (which worked fine) we tried to find the error an excluded (out-commented) an existing Db, but this database stayed in the tools. So the blastdb.loc file seems to be ignored by galaxy. (This is consistent for multiple users and browser, so we are sure this is not a client-sided Browser-Cache issue) So my questions are: Is there any kind of internal Cache in Galaxy which could explain this behavior? How can we track down / solve the issue? Our Galaxy Version is 17.05 Thanks a lot in advance! Mit freundlichen Grüßen i.A. Matthias Enders ********************************** [cid:image002.png@01CF9B54.EBA59810] NPZ Innovation GmbH Hohenlieth-Hof, D-24363 Holtsee Tel. +49-4351-736 189<tel:%2B49-4351-736%20189> Fax +49-4351-736 271<tel:%2B49-4351-736%20271> Mobil: +49-151-14247360<tel:%2B49-0151-14247360> Mail: m.enders(a)npz-innovation.de<mailto:m.enders@npz-innovation.de> Web: www.npz-innovation.de<http://www.npz-innovation.de/> Firmensitz Hohenlieth, Holtsee Amtsgericht Kiel, HRB 15342 Kl Geschäftsführer: Dr. Gunhild Leckband, Thorsten Pommer

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Re: [galaxy-dev] galaxy-dev Digest, Vol 136, Issue 8
by Matthias Enders 18 Oct '17

18 Oct '17

Dear Galaxy Dev List, we currently searching for a good Genome Browser. As we run a local galaxy instance, we noticed the integrated GTB ("Galaxy Track Browser"). So my question is: Is there a roadmap for further support / development of the GTB? Or will it perhaps get replaced/deprecated in the near future (we read a lot of UCSC Genome Browser - Galaxy - Integration)? Another question would be on good sources/tutorials/manuals for configuring and setup for the GTB. Mit freundlichen Grüßen Matthias Enders ----------------------------------------------------------------------- GERMAN SEED ALLIANCE GmbH c/o Norddeutsche Pflanzenzucht Hans-Georg Lembke KG Hohenlieth, 24363 Holtsee Tel.: +49 (0)4351/ 736-189 Fax: + 49 (0)4351/ 736-271 Mobil: +49 (0)151/ 14247360 Email: m.enders(a)german-seed-alliance.de Firmensitz Köln Amtsgericht Köln, HRB 73844

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Problems with the test tool shed?
by Von Kuster, Greg 17 Oct '17

17 Oct '17

Hi all, I’m wondering if the TTS can be restarted. I’ve been seeing this of-and-on all afternoon. Thanks! Galaxy<http://galaxyproject.org/> The Test Tool Shed could not be reached You are seeing this message because a request to The Test Tool Shed timed out or was refused. This may be a temporary issue which could be resolved by retrying the operation you were performing. If you receive this message repeatedly or for an extended amount of time, please contact an administrator.

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primer blast tool
by Jochen Bick 13 Oct '17

13 Oct '17

Hi all, has anyone yet worked on wrapping primer-blast? https://www.ncbi.nlm.nih.gov/tools/primer-blast/ Cheers Jochen -- ETH Zurich *Jochen Bick* Animal Physiology Institute of Agricultural Sciences Postal address: Universitätstrasse 2 / LFW B 58.1 Office: Tannenstrasse 1 / TAN D 6.2 8092 Zurich, Switzerland Phone +41 44 632 28 25 jochen.bick(a)usys.ethz.ch <mailto:jochen.bick@usys.ethz.ch> www.ap.ethz.ch

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Call for presentations at GMOD workshop at PAG
by Scott Cain 12 Oct '17

12 Oct '17

Hi all, This January in San Diego is the annual Plant and Animal Genomes (PAG) meeting (http://www.intlpag.org) As in previous PAGs, there will be several opportunities to present content related to GMOD projects. If you are interested in attending PAG and giving a talk at the GMOD workshop on Wednesday, January 17, please let me know. Your talk can either be about new developments/functionality in existing GMOD software, about how your organization is using the suite of GMOD software to good effect, or about technologies that you think the GMOD community would be interested in hearing about. Please email me directly with a title, an abstract or a vague idea of what you'd like to talk about. Also, if you'd really like to come but are having a hard time coming up with travel funds, please let me know, I might be able to help you with that too (up to a limit of one person anyway). Cheers, Scott -- ------------------------------------------------------------------------ Scott Cain, Ph. D. scott at scottcain dot net GMOD Coordinator (http://gmod.org/) 216-392-3087 Ontario Institute for Cancer Research

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Show history structure : Error 'Undefined' object is not callable
by julie dubois 12 Oct '17

12 Oct '17

Hi all, I'm on 17.05 galaxy version and display it on firefox. I'm trying to use "show structure" functionnality on my histories (I've never tried before this version) and I obtain this error : URL: http://192.168.100.98:8080/galaxy/history/display_structured File '/data/galaxy-dist/.venv/local/lib/python2.7/site-packages/weberror/evalexception.py', line 431 in respond app_iter = self.application(environ, detect_start_response) File '/data/galaxy-dist/.venv/local/lib/python2.7/site-packages/paste/recursive.py', line 85 in __call__ return self.application(environ, start_response) File '/data/galaxy-dist/.venv/local/lib/python2.7/site-packages/paste/httpexceptions.py', line 640 in __call__ return self.application(environ, start_response) File '/data/galaxy-dist/lib/galaxy/web/framework/base.py', line 135 in __call__ return self.handle_request( environ, start_response ) File '/data/galaxy-dist/lib/galaxy/web/framework/base.py', line 214 in handle_request body = method( trans, **kwargs ) File '/data/galaxy-dist/lib/galaxy/webapps/galaxy/controllers/history.py', line 571 in display_structured return trans.fill_template( "history/display_structured.mako", items=items, history=history ) File '/data/galaxy-dist/lib/galaxy/web/framework/webapp.py', line 891 in fill_template return self.fill_template_mako( filename, **kwargs ) File '/data/galaxy-dist/lib/galaxy/web/framework/webapp.py', line 905 in fill_template_mako return template.render( **data ) File '/data/galaxy-dist/.venv/local/lib/python2.7/site-packages/mako/template.py', line 445 in render return runtime._render(self, self.callable_, args, data) File '/data/galaxy-dist/.venv/local/lib/python2.7/site-packages/mako/runtime.py', line 829 in _render **_kwargs_for_callable(callable_, data)) File '/data/galaxy-dist/.venv/local/lib/python2.7/site-packages/mako/runtime.py', line 864 in _render_context _exec_template(inherit, lclcontext, args=args, kwargs=kwargs) File '/data/galaxy-dist/.venv/local/lib/python2.7/site-packages/mako/runtime.py', line 890 in _exec_template callable_(context, *args, **kwargs) File '/data/galaxy-dist/database/compiled_templates/base.mako.py', line 63 in render_body __M_writer(unicode(next.body())) File '/data/galaxy-dist/database/compiled_templates/history/display_structured.mako.py', line 50 in render_body __M_writer(unicode(render_item( entity, children ))) File '/data/galaxy-dist/database/compiled_templates/history/display_structured.mako.py', line 35 in render_item return render_render_item(context._locals(__M_locals),entity,children) File '/data/galaxy-dist/database/compiled_templates/history/display_structured.mako.py', line 191 in render_render_item render_item_job( entity, children ) File '/data/galaxy-dist/database/compiled_templates/history/display_structured.mako.py', line 183 in render_item_job return render_render_item_job(context,job,children) File '/data/galaxy-dist/database/compiled_templates/history/display_structured.mako.py', line 239 in render_render_item_job __M_writer(unicode( show_params.inputs_recursive( tool.inputs, params_object, depth=1 ) )) File '/data/galaxy-dist/database/compiled_templates/show_params.mako.py', line 293 in render_inputs_recursive for i, element in enumerate(listify(param_values[input.name])): TypeError: 'Undefined' object is not callable Is it a problem with this history (I've tested with a full green history and with history containing red jobs without difference in error message) or with my galaxy configuration may be ? Thanks. Julie

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another conda problem
by Matthias Bernt 12 Oct '17

12 Oct '17

Dear list, thanks for giving me a workaround for yesterdays conda problem. Today I got a new one: I tried to install RSeQC which installs (including the dependencies) without reporting an error in the galaxy admin UI. But actually the package is not installed, e.g. infer_experiment.py can not be found in the environment. When I check the galaxy logs I find the following: `Installing conda-forge::wheel-0.30.0-py_1 requires a minimum conda version of 4.3.` Can I safely update conda to version 4.3? Galaxy's conda FAQ https://docs.galaxyproject.org/en/master/admin/conda_faq.html suggests 4.2.13? Is the successful reporting of the installation a bug? Cheers, Matthias -- ------------------------------------------- Matthias Bernt Bioinformatics Service Molekulare Systembiologie (MOLSYB) Helmholtz-Zentrum für Umweltforschung GmbH - UFZ/ Helmholtz Centre for Environmental Research GmbH - UFZ Permoserstraße 15, 04318 Leipzig, Germany Phone +49 341 235 482296, m.bernt(a)ufz.de, www.ufz.de Sitz der Gesellschaft/Registered Office: Leipzig Registergericht/Registration Office: Amtsgericht Leipzig Handelsregister Nr./Trade Register Nr.: B 4703 Vorsitzender des Aufsichtsrats/Chairman of the Supervisory Board: MinDirig Wilfried Kraus Wissenschaftlicher Geschäftsführer/Scientific Managing Director: Prof. Dr. Dr. h.c. Georg Teutsch Administrative Geschäftsführerin/ Administrative Managing Director: Prof. Dr. Heike Graßmann -------------------------------------------

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conda bash environment problem as real user
by Matthias Bernt 11 Oct '17

11 Oct '17

Dear list, our galaxy runs jobs as real user and I get the following error for multiple tools: """ Failed to activate conda environment! Error was: CondaEnvironmentError: Environment error: Cannot activate environment bash. User does not have write access for conda symlinks. Fatal error: Exit code 1 () """ Does anyone have an idea where I could start digging? My workaround (run the tool once as galaxy user) is to time consuming since I have to restart galaxy 2x. Thanks a lot. Cheers, Matthias P.S.: https://github.com/galaxyproject/galaxy/issues/4767 -- ------------------------------------------- Matthias Bernt Bioinformatics Service Molekulare Systembiologie (MOLSYB) Helmholtz-Zentrum für Umweltforschung GmbH - UFZ/ Helmholtz Centre for Environmental Research GmbH - UFZ Permoserstraße 15, 04318 Leipzig, Germany Phone +49 341 235 482296, m.bernt(a)ufz.de, www.ufz.de Sitz der Gesellschaft/Registered Office: Leipzig Registergericht/Registration Office: Amtsgericht Leipzig Handelsregister Nr./Trade Register Nr.: B 4703 Vorsitzender des Aufsichtsrats/Chairman of the Supervisory Board: MinDirig Wilfried Kraus Wissenschaftlicher Geschäftsführer/Scientific Managing Director: Prof. Dr. Dr. h.c. Georg Teutsch Administrative Geschäftsführerin/ Administrative Managing Director: Prof. Dr. Heike Graßmann -------------------------------------------

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Announcing the Galactic Blog, and a call for posts
by Dave Clements 05 Oct '17

05 Oct '17

Hello all, I am pleased to announce the *Galactic Blog <https://galaxyproject.org/blog/>,* a place for blogging about Galaxy and your experiences with it. The blog is on the Galaxy Hub <https://galaxyproject.org/> and can be reached from the home page and the Hub's Community menu. Our very first post <https://galaxyproject.org/blog/2017-10-05-elixir-galaxy-community/> is about the ELIXIR Galaxy Community and was written by Frederik Coppens, Gildas Le Corguillé, and Björn Grüning. We have a few more posts lined up over the next week or so, but after that ... *The Galactic Blog needs you! *If you've done something that others would benefit from knowing about then please create a Galactic Blog post describing your experiences. See the CONTRIBUTING <https://github.com/galaxyproject/galaxy-hub/blob/master/CONTRIBUTING.md#blo…> page. If you have questions, please let me know. Blog posts can either be directly created in the Galactic Blog (and hosted on the Galaxy Hub <https://galaxyproject.org/>), or can be posted on your favorite blogging platform (see, for example, Galactic Engineer <http://galacticengineer.blogspot.co.uk/>) and linked to from the Galactic Blog. We'll tweet about every entry and highlight them in the monthly newsletter as well. Finally, this was a team effort and I'd particularly like to thank Dannon Baker, Björn Grüning, and Martin Čech for their contributions. I look forward to reading your blog posts! Dave C PS: The Galactic Blog replaces the former *Community Log* and includes all content from it (which is why, even though the blog is new, it includes entries back to 2013). -- https://galaxyproject.org/ https://usegalaxy.org/

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