August 2018 - galaxy-dev - lists.galaxyproject.org

one dataset won't import
by Langhorst, Brad 10 Aug '18

10 Aug '18

Hi Galaxy folks: We have one data set in a shared library that will not import to a history. I am able to import it using the page for that dataset, but not from the list of all datasets in the folder. I’m not sure the source of the error - this particular row does not look odd to me.= Any Ideas? here’s a row that will import: <tr class="dataset_row light library-row" data-id="e369c8b86fc4c943" style="display: table-row;"><td><span title="Dataset" class="fa fa-file-o"></span></td><td style="text-align: center; "><input style="margin: 0;" type="checkbox"></td><td><a href="#folders/F09026885d1dcbcc0/datasets/e369c8b86fc4c943" class="library-dataset">MM809_9_x4_B5.1.fastq</a><a></a></td><td></td><td>fastqsanger</td><td>31.5 MB</td><td>2018-08-10 02:38 PM</td><td></td><td><span data-toggle="tooltip" data-placement="top" title="" style="color:grey;" class="fa fa-globe fa-lg" data-original-title="Unrestricted dataset"></span><a href="#folders/F09026885d1dcbcc0/datasets/e369c8b86fc4c943/permissions"><button data-toggle="tooltip" data-placement="top" class="primary-button btn-xs permissions-dataset-btn" title="" data-original-title="Permissions of 'MM809_9_x4_B5.1.fastq'"><span class="fa fa-group"></span> Manage</button></a></td></tr> here’s one that will not: <td><span title="Dataset" class="fa fa-file"></span></td><td style="text-align: center; "><input style="margin: 0;" type="checkbox"></td><td><a href="#folders/F09026885d1dcbcc0/datasets/7582870467626242" class="library-dataset dark">MM809_9_x4_B5.2.fastq</a><a class="dark"></a></td><td></td><td>fastqsanger</td><td>31.5 MB</td><td>2018-08-10 02:38 PM</td><td></td><td><span data-toggle="tooltip" data-placement="top" title="" style="color:grey;" class="fa fa-globe fa-lg" data-original-title="Unrestricted dataset"></span><a href="#folders/F09026885d1dcbcc0/datasets/7582870467626242/permissions" class="dark"><button data-toggle="tooltip" data-placement="top" class="primary-button btn-xs permissions-dataset-btn" title="" data-original-title="Permissions of 'MM809_9_x4_B5.2.fastq'"><span class="fa fa-group"></span> Manage</button></a></td> here’s the error in the js console: TypeError: n.substring is not a function[Learn More] library-foldertoolbar-view.js:1205:16<webpack:///galaxy/scripts/mvc/library/library-foldertoolbar-view.js> findCheckedItems/< library-foldertoolbar-view.js:1205:16<webpack:///galaxy/scripts/mvc/library/library-foldertoolbar-view.js> each jquery.js:365<webpack:///galaxy/scripts/libs/jquery/jquery.js> each jquery.js:137<webpack:///galaxy/scripts/libs/jquery/jquery.js> findCheckedItems library-foldertoolbar-view.js:1201:8<webpack:///galaxy/scripts/mvc/library/library-foldertoolbar-view.js> processImportToHistory library-foldertoolbar-view.js:283:28<webpack:///galaxy/scripts/mvc/library/library-foldertoolbar-view.js> importAllIntoHistory library-foldertoolbar-view.js:272:12<webpack:///galaxy/scripts/mvc/library/library-foldertoolbar-view.js> Import library-foldertoolbar-view.js:231:32<webpack:///galaxy/scripts/mvc/library/library-foldertoolbar-view.js> dispatch jquery.js:4736<webpack:///galaxy/scripts/libs/jquery/jquery.js> e.dispatch jquery.event.drag.js:377<webpack:///galaxy/scripts/libs/jquery/jquery.event.drag.js> add/m.handle jquery.js:4549<webpack:///galaxy/scripts/libs/jquery/jquery.js>

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links to UCSC Genome Browser dev server
by Dave Clements 10 Aug '18

10 Aug '18

Hi All, If you run a Galaxy server and that server links to the UCSC Genome Browser *development* server, then you will need to update the URL you link to. See below for details from Ann Zweig at UCSC. I am writing because a few of your servers provide links to the UCSC Genome > Browser development server at genome-test.*cse*.ucsc.edu or genome-test. > *soe*.ucsc.edu (see list below). This weekend we are retiring that server > and bringing it back to life next week with a new name: genome-test.*gi*. > ucsc.edu. Cheers, Dave C -- https://galaxyproject.org/ https://usegalaxy.org/

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Native LDAP auth to AD
by RSD 06 Aug '18

06 Aug '18

I am running into issues configuring galaxy to auth against Active Directory. The search user i have configured works for searching, but when it goes to bind, it fails. Yes, i am using ldaps over ssl to the global catalog ssl port...

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Gateways 2018: Early-bird ENDS Aug. 6; Poster Session EXTENSION to Aug. 15
by Katherine Lawrence 03 Aug '18

03 Aug '18

* Gateways 2018Tuesday through Thursday, September 25–27, 2018Hosted at the University of Texas, Austin *https://sciencegateways.org/gateways2018* The Gateways annual conference is an opportunity for gateway creators and enthusiasts (such as those who use the Galaxy platform) to learn, share, connect, and shape the future of gateways. Theconference program <https://sciencegateways.org/web/gateways2018/program>is already brimming with exciting keynotes, tutorials, and sessions. Early-bird registration <https://sciencegateways.org/web/gateways2018/attend/register>is open through Monday, August 6.(Regular registration and hotel block rate close Friday, Sept. 7.) Travel Support Grants <https://sciencegateways.org/web/gateways2018/attend/travel-support>are available for both students and non-students. Apply by August 10! Anyone is welcome to participate in the Poster Session.<https://sciencegateways.org/web/gateways2018/program/cfp#poster>The deadline to submit an abstract for your poster has been extended to Wed., August 15 <https://sciencegateways.org/web/gateways2018/program/cfp#poster>. Do you or a colleague offer resources or services that would be of interest to the science gateways community?Consider reserving a space at the Resource Expo, to be held on the evening of Wednesday, Sept. 26. It's an opportunity to showcase products and services, network with attendees, and recruit individuals eager to pursue careers in the field. For more information, visit *<https://sciencegateways.org/web/gateways2018/program/resource-expo>https://sciencegateways.org/web/gateways2018/program <https://sciencegateways.org/web/gateways2018/program/resource-expo>/resource-expo <https://sciencegateways.org/web/gateways2018/program/resource-expo>.* <https://sciencegateways.org/web/gateways2018/program/resource-expo> Questions? Email help(a)sciencegateways.org.*

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August Galaxy News: GCC2019, Online GTN CoFest, new pubs, servers, tools...
by Dave Clements 02 Aug '18

02 Aug '18

Hello all, After a two-month hiatus, the August 2018 Galactic News <https://galaxyproject.org/galaxy-updates/2018-08/> is out! Here are some of the highlights: - GCCBOSC 2018 <https://galaxyproject.org/galaxy-updates/2018-08/#gccbosc-2018-is-done> has come and gone, *and the numbers were impressive* - GCC2019 <https://galaxyproject.org/galaxy-updates/2018-08/#2019-galaxy-community-con…> will be held in Freiburg, Germany, 1-6 July - What about BOSC? <https://galaxyproject.org/galaxy-updates/2018-08/#what-about-bosc>, you ask - Other event news: - GTN CoFest on Metagenomics Training Material <https://galaxyproject.org/galaxy-updates/2018-08/#gtn-cofest-on-metagenomic…>, 17 August, *online* - 2018 SACNAS Workshops <https://galaxyproject.org/galaxy-updates/2018-08/#2018-sacnas-workshops> - European Galaxy Days <https://galaxyproject.org/galaxy-updates/2018-08/#european-galaxy-days-19-2…>, 19-20 November, Freiburg, Germany - Gateways 2018 <https://galaxyproject.org/galaxy-updates/2018-08/#gateways-2018> early bird deadline *is Monday*. - Other Upcoming events <https://galaxyproject.org/galaxy-updates/2018-08/#upcoming-events> (on three continents in 6 countries) - Christophe Caron, 1968-2018 <https://galaxyproject.org/galaxy-updates/2018-08/#christophe-caron-1968-2018> - New: - 417 publications <https://galaxyproject.org/galaxy-updates/2018-08/#publications> (that's 3 month's worth) - Two Galactic Blog entries <https://galaxyproject.org/galaxy-updates/2018-08/#new-galactic-blog-entries>, including the first ever *Contributor of the Month* posting. - Public Galaxy Server News <https://galaxyproject.org/galaxy-updates/2018-08/#public-galaxy-server-news>: ProteoRE - ToolShed contributions <https://galaxyproject.org/galaxy-updates/2018-08/#toolshed-contributions> - Hub and Documentation updates <https://galaxyproject.org/galaxy-updates/2018-08/#hub-and-doc-updates> - Releases <https://galaxyproject.org/galaxy-updates/2018-08/#releases> of Galaxy, Planemo, galaxy-lib, ephemeris, and sequence_utils. - And other news <https://galaxyproject.org/galaxy-updates/2018-08/#other-news> too See the newsletter <https://galaxyproject.org/galaxy-updates/2018-08/> for the full story. Thanks for using Galaxy! -- https://galaxyproject.org/ https://usegalaxy.org/

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Hierarchical upload API documentation and example
by Lance Parsons 01 Aug '18

01 Aug '18

Hi all, I’ve been looking at the new hierarchical upload API and I’d like to try and use it to integrate our existing sequence data repository a bit better with Galaxy. Currently I use a tool to post data to Galaxy, which works, but seems a bit clunky. This seems more built in and future proof. I’ve seen the discussion on galaxyproject/galaxy#5220 <https://github.com/galaxyproject/galaxy/pull/5220> but I was wondering if there was any other, more formal, documentation. Or possibly anyone who has actually implemented (or started to implement) anything using this. Thanks! I’ve also seen the tutorial linked in the release notes <https://github.com/jmchilton/training-material/blob/rules/topics/introducti…> but I was wondering where that is actually hosted for public consumption. I’m a bit lost with the various places for Galaxy documentation and training these days… -- Lance Parsons - Scientific Programmer Carl C. Icahn Laboratory - Room 136 Lewis-Sigler Institute for Integrative Genomics Princeton University

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