- galaxy-dev - lists.galaxyproject.org

drmaa chown sudo
by Matthias Bernt 12 Apr '17

12 Apr '17

Dear galaxy-dev list, The documentation (https://galaxyproject.org/admin/config/performance/cluster/) mentions that sudo permissions for /usr/bin/chown are required in order to run jobs as a real user. This causes quite some headache to our system admins (understandably). I tried (unsuccessfully) to dig a bit in the sources to find the place(s) where sudo chown is called (the idea was to create a small wrapper which might get sudo permissions). But I found that there is already scripts/external_chown_script.py (which is also referred in galaxy.ini). Is it sufficient to make this script sudo callable? Or where could I invoke a wrapper for sudo chown in the galaxy code? Thanks a lot. Best regards, 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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Fwd: [Bosc] BOSC 2017: Call for Abstracts
by Peter Cock 10 Apr '17

10 Apr '17

Dear all, Recent BOSC meetings have had a strong Galaxy presence, so please do consider submitting an abstract and/or attending BOSC 2017 in Prague. Thank you, Peter Dr. Peter Cock, Bioinformatician at The James Hutton Institute; Open Bioinformatics Foundation, board of directors, treasurer; BOSC 2017 organising committee member. ---------- Forwarded message ---------- From: Nomi Harris <nlharris(a)gmail.com> Date: Mon, Mar 6, 2017 at 6:50 PM Subject: [Bosc] BOSC 2017: Call for Abstracts To: bosc-announce(a)mailman.open-bio.org, bosc-reviewers(a)open-bio.org Cc: Nomi Harris <nlharris(a)gmail.com>, BOSC 2017 Organizing Committee < bosc(a)open-bio.org> *Call for Abstracts for the 18th Annual Bioinformatics Open Source Conference (BOSC 2017)* An ISMB/ECCB Community of Special Interest (COSI) Dates: July 22-23, 2017 Location: Prague, Czech Republic Web site: http://www.open-bio.org/wiki/BOSC_2017 Email: bosc(a)open-bio.org BOSC announcements mailing list: http://lists.open-bio. org/mailman/listinfo/bosc-announce Twitter: @OBF_BOSC *Important Dates* - Call for one-page abstracts <https://www.open-bio.org/wiki/BOSC_Abstract_Submission> opens: March 6, 2017 - Abstract submission <https://www.open-bio.org/wiki/BOSC_Abstract_Submission> deadline: April 13, 2017 - Travel fellowship <https://github.com/OBF/obf-docs/blob/master/Travel_fellowships.md> application deadline: April 15, 2017 - Authors notified: May 10, 2017 - Codefest 2017 <https://www.open-bio.org/wiki/Codefest_2017>: July 21-22, Prague - BOSC 2017 <https://www.open-bio.org/wiki/BOSC_2017>: July 22-23, Prague (days 1 and 2 of ISMB/ECCB) - ISMB/ECCB 2017 <https://www.iscb.org/ismbeccb2017>: July 21-25, Prague *About BOSC* Since 2000, the yearly Bioinformatics Open Source Conference (BOSC) has provided a forum for developers and users to interact and share research results and ideas in open source bioinformatics. BOSC’s broad spectrum of topics includes practical techniques for solving bioinformatics problems; software development practices; standards and ontologies; approaches that promote open science and sharing of data, results and software; and ways to grow open source communities while promoting diversity within them. In the past, BOSC has taken place the two days before ISMB as a Special Interest Group (SIG). This year, ISMB is trying a new structure: the SIGs (now called COSIs) are integrated into the main ISMB meeting. BOSC will take place the first two full days of ISMB (July 22-23). Attendees will have the option to register for the full ISMB/ECCB meeting (July 21-25) or for just two days (there is no single-day registration option this year). A limited number of partial travel fellowships will be granted to some accepted speakers who would not otherwise be able to attend BOSC--please see https://github.com/OBF/obf-docs/blob/master/Travel_fellowships.md for more information. We encourage you to submit one-page abstracts on any topic of relevance to open source bioinformatics and open science. After review, some abstracts will be selected for lightning talks, longer talks, and/or posters. Abstract submission instructions and a link to the EasyChair portal can be found on https://www.open-bio.org/wiki/BOSC_Abstract_Submission *Session topics include:* - Open Science and Reproducible Research - Open Biomedical Data - Citizen/Participatory Science - Standards and Interoperability - Data Science - Workflows - Visualization - Medical and Translational Bioinformatics - Developer Tools and Libraries - Bioinformatics Open Source Project Progress Reports *Sponsorship* We gratefully accept sponsorships from relevant private companies. These sponsorships enable us to offer free registration to some BOSC speakers to help increase diversity at our meeting. Sponsors in 2016 included Curoverse, the company behind the open source platform Arvados. Please contact us if you are interested in being a sponsor of BOSC 2017! Thank you, BOSC 2017 Organizing Committee: Nomi Harris (chair), Brad Chapman, Peter Cock, Christopher Fields, Bastian Greshake, Karsten Hokamp, Hilmar Lapp, Mónica Muñoz-Torres, Heather Wiencko P.S. Don't forget to submit your BOSC abstract by April 13 at https://www.open-bio.org/wiki/BOSC_Abstract_Submission! -- You received this message because you are subscribed to the Google Groups "OBF-BOSC" group. To unsubscribe from this group and stop receiving emails from it, send an email to obf-bosc+unsubscribe(a)googlegroups.com. Visit this group at https://groups.google.com/group/obf-bosc. For more options, visit https://groups.google.com/d/optout.

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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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Login message
by Timo Janßen 05 Apr '17

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 04 Apr '17

04 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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SLURM configuration problem
by Leonor Palmeira 31 Mar '17

31 Mar '17

Dear all, we have setup a Galaxy instance on a virtual machine, and we want to be able to submit jobs to our HPC system (SLURM). Currently, we do not understand how to define that jobs will be sent to the HPC cluster. We have set : export $DRMAA_LIBRARY_PATH=/var/lib/libdrmaa.so This is our config/job_conf.xml : <?xml version="1.0"?>  <job_conf> <plugins> <plugin id="drmaa" type="runner" load="galaxy.jobs.runners.drmaa:DRMAAJobRunner" /> </plugins> <handlers default="handlers"> <handler id="handler0" tags="handlers" /> <handler id="main" /> </handlers> <destinations default="slurm"> <destination id="slurm" runner="drmaa"> <param id="nativeSpecification">-P all_5hrs</param> </destination> </destinations> </job_conf> And the output of "sh run.sh" : galaxy.jobs.manager DEBUG 2017-02-07 15:50:39,962 Starting job handler galaxy.jobs INFO 2017-02-07 15:50:39,962 Handler 'main' will load all configured runner plugins galaxy.jobs.runners.state_handler_factory DEBUG 2017-02-07 15:50:39,971 Loaded 'failure' state handler from module galaxy.jobs.runners.state_handlers.resubmit pulsar.managers.util.drmaa DEBUG 2017-02-07 15:50:39,975 Initializing DRMAA session from thread MainThread Traceback (most recent call last): File "/home/mass/GAL/APP/galaxy/lib/galaxy/webapps/galaxy/buildapp.py", line 55, in paste_app_factory app = galaxy.app.UniverseApplication( global_conf=global_conf, **kwargs ) File "/home/mass/GAL/APP/galaxy/lib/galaxy/app.py", line 170, in __init__ self.job_manager = manager.JobManager( self ) File "/home/mass/GAL/APP/galaxy/lib/galaxy/jobs/manager.py", line 23, in __init__ self.job_handler = handler.JobHandler( app ) File "/home/mass/GAL/APP/galaxy/lib/galaxy/jobs/handler.py", line 32, in __init__ self.dispatcher = DefaultJobDispatcher( app ) File "/home/mass/GAL/APP/galaxy/lib/galaxy/jobs/handler.py", line 723, in __init__ self.job_runners = self.app.job_config.get_job_runner_plugins( self.app.config.server_name ) File "/home/mass/GAL/APP/galaxy/lib/galaxy/jobs/__init__.py", line 687, in get_job_runner_plugins rval[id] = runner_class( self.app, runner[ 'workers' ], **runner.get( 'kwds', {} ) ) File "/home/mass/GAL/APP/galaxy/lib/galaxy/jobs/runners/drmaa.py", line 88, in __init__ self.ds = DrmaaSessionFactory().get() File "/usr/local/lib/python2.7/dist-packages/pulsar/managers/util/drmaa/__init__.py", line 31, in get return DrmaaSession(session_constructor, **kwds) File "/usr/local/lib/python2.7/dist-packages/pulsar/managers/util/drmaa/__init__.py", line 49, in __init__ DrmaaSession.session.initialize() File "/usr/local/lib/python2.7/dist-packages/drmaa/session.py", line 257, in initialize py_drmaa_init(contactString) File "/usr/local/lib/python2.7/dist-packages/drmaa/wrappers.py", line 73, in py_drmaa_init return _lib.drmaa_init(contact, error_buffer, sizeof(error_buffer)) File "/usr/local/lib/python2.7/dist-packages/drmaa/errors.py", line 151, in error_check raise _ERRORS[code - 1](error_string) InternalException: code 1: cell directory "/usr/lib/gridengine-drmaa/default" doesn't exist Could anyone point us in the right direction? This would be greatly appreciated. Best regards Leonor -- Leonor Palmeira | PhD Associate Scientist Department of Human Genetics CHU de Liège | Domaine Universitaire du Sart-Tilman 4000 Liège | BELGIQUE Tél: +32-4-366.91.41 Fax: +32-4-366.72.61 e-mail: lpalmeira(a)chu.ulg.ac.be

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