galaxy-dev April 2017

galaxy-dev@lists.galaxyproject.org

16 participants
27 discussions

git clone 16.10 bwa 0.7.15 data manager
by Bryan Hepworth 10 Apr '17

10 Apr '17

Hi All I've been trying to get a local galaxy running with an assortment of tools for a local researcher. I'm a linux administrator rather than a bioinformatics researcher and am familiar with how repo's work for RedHat, R and the like. I've built tools for other groups at work and from my reading it looked like galaxy was working on similar lines for keeping things in step. I've done a git clone of 16.10 into /galaxy altered the galaxy.ini to postgresql and added me as admin. Done the sh run.sh to get a feel for how everything goes together. I've pulled reference genomes from the source and have had some success converting to different formats. I bumped up against a few dependency issues so I've also enabled the test repo. The first stumbling block on the most recent build is getting bwa on there with the data manager route - it has a dependency on bwa 0.7.15, but try as I might I don't seem to be able to find an instance of package_bwa_0.7.15 anywhere on the devteam repo's to get over this hurdle. I'm guessing I'm missing something really simple as it isn't pulling in dependancies as the documentation suggests it should. I'd be really grateful for any pointers. Bryan

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galaxy startup errors and warnings
by Matthias Bernt 10 Apr '17

10 Apr '17

Dear list, I get two messages where I do not know how to continue: The first seems to be severe: tool_shed.util.common_util WARNING 2017-04-10 07:37:39,800 The URL https://toolshed.g2.bx.psu.edu/repository/get_repository_dependencies?owner… raised the exception: <urlopen error [SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed (_ssl.c:661)> tool_shed.galaxy_install.migrate.check DEBUG 2017-04-10 07:37:39,800 The main Galaxy tool shed is not currently available, so skipped tool migration 1 until next server startup What could I do to debug this? The other one seems to be easy to fix: galaxy.tools.deps.resolvers.conda WARNING 2017-04-10 07:33:27,435 Conda install prefix '/gpfs1/data/galaxy_server/galaxy-dev/database/dependencies/_conda' is 65 characters long, this can cause problems with package installation, consider setting a shorter prefix (conda_prefix in galaxy.ini) My idea would be to setup a symbolic link which leads to a shorter prefix. Are there better suggestions? Could somebody give me a pointer to understand the reason for the potential problems? 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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cytoscape & charts
by Matthias Bernt 05 Apr '17

05 Apr '17

Dear galaxy-dev, I just wanted to test the exciting cytoscape charts plugin that was just announced: https://github.com/galaxyproject/galaxy/pull/3817 So I created a small sif file nodeA xx nodeB nodeB xx nodeC nodeC xx nodeD nodeD xx nodeA nodeB xx nodeD I guess I have to click the "Visualize" button of the data set where I have the options "Charts" and "Graph Visualizations". The former has only oine option: Multiple Sequence Alignment (BioJS). So I guess its the latter which shows me a graph. But it looks different to the example in the pull request, e.g. node names are not shown and I can not interact as shown in the three figures. Is there some docomentation that I could read. In general I would be interested to read about the Charts. Would be grateful about some pointers. 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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05 Apr '17

Hi, is it possible to change the message that is shown on the login page? At the moment it says "This Galaxy instance has been configured such that only users who are logged in may use it. If you don't already have an account, you may create one." I looked for the file where the text is defined but couldn't find it. Best regards, Timo -- ------------------------------------------------------------------------ Timo Janßen Wissenschaftliche Hilfskraft Arbeitsgruppe "Anwendungs- und Informationssysteme" Tel.: +49(0)551/201-1791 E-Mail: timo.janssen(a)gwdg.de ------------------------------------------------------------------------ Gesellschaft für wissenschaftliche Datenverarbeitung mbH Göttingen (GWDG) Am Faßberg 11, 37077 Göttingen, URL: http://www.gwdg.de Tel.: +49 551 201-1510, Fax: +49 551 201-2150, E-Mail: gwdg(a)gwdg.de Service-Hotline: Tel.: +49 551 201-1523, E-Mail: support(a)gwdg.de Geschäftsführer: Prof. Dr. Ramin Yahyapour Aufsichtsratsvorsitzender: Prof. Dr. Norbert Lassau Sitz der Gesellschaft: Göttingen Registergericht: Göttingen, Handelsregister-Nr. B 598 ------------------------------------------------------------------------ Zertifiziert nach ISO 9001 ------------------------------------------------------------------------

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Galaxy Pbs Pro drmaav2
by Laure QUINTRIC 05 Apr '17

05 Apr '17

Hi there, I am currently using Galaxy with the deprecated DRMAAV1 to submit jobs on pbs pro cluster. Altair just released an implementation of DRMAAV2 for PBS pro (see doc below). Do you think it is compatible with Galaxy ? Has anyone tried ? https://pbspro.atlassian.net/wiki/display/PD/DRMAAV2-3+%3A+DRMAAv2+implemen… https://github.com/PBSPro/DRMAAv2 Thanks for feedback. Best Regards, Laure

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April 2017 Galaxy News: GCC2017 + new events, papers, jobs, servers, releases, and a milestone
by Dave Clements 05 Apr '17

05 Apr '17

Hello all, The April 2017 Galaxy News <https://galaxyproject.org/galaxy-updates/2017-04/> is out! - Usegalaxy.org passes a milestone <https://galaxyproject.org/galaxy-updates/2017-04/#usegalaxy-org-passes-100-…> - 2017 Galaxy Community Conference <https://galaxyproject.org/galaxy-updates/2017-04/#2017-galaxy-community-con…> early registration and abstract submission are open. - Travel fellowships for GCC2017 <https://galaxyproject.org/galaxy-updates/2017-04/#gcc2017-travel-fellowships> are available from the Galaxy Community Fund *(apply by April 5!)*. - New GCC2017 Sponsors: ELIXIR and GigaScience <https://galaxyproject.org/galaxy-updates/2017-04/#new-gcc2017-sponsors> - G-OnRamp Beta Testers Workshop: Invitation <https://galaxyproject.org/galaxy-updates/2017-04/#g-onramp-beta-testers-wor…> - A whole lot more <https://galaxyproject.org/galaxy-updates/2017-04/#all-upcoming-events> events are coming up. - 275 new publications <https://galaxyproject.org/galaxy-updates/2017-04/#new-publications>, including 12 highlighted pubs. - Four open positions <https://galaxyproject.org/galaxy-updates/2017-04/#who-s-hiring> in Europe and North America. - Two new public servers, LAPPS Grid looking for collaborators, new PhenoMeNal training material <https://galaxyproject.org/galaxy-updates/2017-04/#public-galaxy-server-news> - New releases <https://galaxyproject.org/galaxy-updates/2017-04/#releases> of CloudBridge, Planemo, and galaxy-lib. - Over 200 new repos <https://galaxyproject.org/galaxy-updates/2017-04/#toolshed-contributions> in the Galaxy Tool Shed. - And other news <https://galaxyproject.org/galaxy-updates/2017-04/#other-news> too. Happy April from the Galaxy Team and Community -- http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/

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"Execute" button does nothing in the CrossMap tool?
by Devon Ryan 03 Apr '17

03 Apr '17

Hi everyone, I'm observing a very odd problem that presumably has something to do with upgrading to Galaxy 17.01 on Friday. Since then, the "Execute" button on the CrossMap tools (from yhoogstrate) does nothing. Upon checking the server logs and the firefox console it looks like there's not even a request sent to Galaxy when a user clicks on the "Execute" button. I recall that the tools worked before, so I can only presume that this is related to the upgrade to 17.01. Has anyone observed anything similar or have suggestions regarding where to start debugging this? I'll note that the user that reported this has tried multiple browsers (firefox and safari) with the same result (nothing happening) in both. Devon -- Devon Ryan, Ph.D. Email: dpryan(a)dpryan.com Data Manager/Bioinformatician Max Planck Institute of Immunobiology and Epigenetics Stübeweg 51 79108 Freiburg Germany

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galaxy-dev April 2017