- galaxy-dev - lists.galaxyproject.org

run.sh problem
by Matthias Bernt 09 Jan '19

09 Jan '19

Dear all, a colleague tries to run.sh on a Manjaro Linux and got the following error: ``` yarn run v1.12.3 $ NODE_ENV=production gulp staging && concurrently "yarn run style" "yarn run webpack-production-maps" "yarn run gulp clean && yarn run gulp-production-maps" && yarn run save-build-hash gulp[12888]: ../src/node_contextify.cc:628:static void node::contextify::ContextifyScript::New(const v8::FunctionCallbackInfo<v8::Value>&): Assertion `args[1]->IsString()' failed. 1: 0x8daaa0 node::Abort() [gulp] 2: 0x8dab75 [gulp] 3: 0x90e2f7 node::contextify::ContextifyScript::New(v8::FunctionCallbackInfo<v8::Value> const&) [gulp] 4: 0xb5e71b [gulp] 5: 0xb606b2 v8::internal::Builtin_HandleApiCall(int, v8::internal::Object**, v8::internal::Isolate*) [gulp] 6: 0x6f20bcdbe1d /tmp/yarn--1546955496175-0.8677740791371564/node: line 3: 12888 Aborted (core dumped) "/home/henning/nextcloud/PhD/20190108-galaxy_workshop/galaxy/.venv/bin/node" "$@" error Command failed with exit code 134. info Visit https://yarnpkg.com/en/docs/cli/run for documentation about this command. ERROR: Galaxy client build failed. See ./client/README.md for more information, including how to get help. Problem running Galaxy command []. Traceback (most recent call last): File "/home/henning/nextcloud/PhD/20190108-galaxy_workshop/galaxy/env/bin/planemo", line 11, in <module> sys.exit(planemo()) File "/home/henning/nextcloud/PhD/20190108-galaxy_workshop/galaxy/env/lib/python3.7/site-packages/click/core.py", line 764, in __call__ return self.main(*args, **kwargs) File "/home/henning/nextcloud/PhD/20190108-galaxy_workshop/galaxy/env/lib/python3.7/site-packages/click/core.py", line 717, in main rv = self.invoke(ctx) File "/home/henning/nextcloud/PhD/20190108-galaxy_workshop/galaxy/env/lib/python3.7/site-packages/click/core.py", line 1137, in invoke return _process_result(sub_ctx.command.invoke(sub_ctx)) File "/home/henning/nextcloud/PhD/20190108-galaxy_workshop/galaxy/env/lib/python3.7/site-packages/click/core.py", line 956, in invoke return ctx.invoke(self.callback, **ctx.params) File "/home/henning/nextcloud/PhD/20190108-galaxy_workshop/galaxy/env/lib/python3.7/site-packages/click/core.py", line 555, in invoke return callback(*args, **kwargs) File "/home/henning/nextcloud/PhD/20190108-galaxy_workshop/galaxy/env/lib/python3.7/site-packages/click/decorators.py", line 64, in new_func return ctx.invoke(f, obj, *args, **kwargs) File "/home/henning/nextcloud/PhD/20190108-galaxy_workshop/galaxy/env/lib/python3.7/site-packages/click/core.py", line 555, in invoke return callback(*args, **kwargs) File "/home/henning/nextcloud/PhD/20190108-galaxy_workshop/galaxy/env/lib/python3.7/site-packages/planemo/cli.py", line 195, in handle_blended_options return f(*args, **kwds) File "/home/henning/nextcloud/PhD/20190108-galaxy_workshop/galaxy/env/lib/python3.7/site-packages/planemo/commands/cmd_serve.py", line 43, in cli galaxy_serve(ctx, runnables, **kwds) File "/home/henning/nextcloud/PhD/20190108-galaxy_workshop/galaxy/env/lib/python3.7/site-packages/planemo/galaxy/serve.py", line 22, in serve return _serve(ctx, runnables, **kwds) File "/home/henning/nextcloud/PhD/20190108-galaxy_workshop/galaxy/env/lib/python3.7/site-packages/planemo/galaxy/serve.py", line 54, in _serve raise Exception(message) Exception: Problem running Galaxy command []. ``` Would be great to have a suggestion... 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 -------------------------------------------

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Forgotten password
by Dalibor Miklík 07 Jan '19

07 Jan '19

Hello, recently I tried to login to my Galaxy account but, obviously, I forgot my password and I can't reset it because I didn't receive any email from the webpage. Can you please help me? Best regards Dalibor Miklik

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January 2019 Galactic News: Events (Admin Training, PAG, GSOC, GCC, GalaxyAdmins), Platforms, Pubs, Jobs, COTM!, Doc, Training, Tools, Releases and more!
by Mo Heydarian 05 Jan '19

05 Jan '19

Hello All, Happy New Year! The *January 2019 Galactic News* is here! This is a summary of what is going on in the Galaxy community. Here's what's happening: - Event News <https://galaxyproject.org/news/2019-01-galaxy-update/#event-news> - 2019 Galaxy Admin Training: Registration is still open! <https://galaxyproject.org/news/2019-01-galaxy-update/#2019-galaxy-admin-tra…> - Training topic nomination for GCC2019 Training extended through 15 January! <https://galaxyproject.org/news/2019-01-galaxy-update/#gcc2019-training-topi…> - Galaxy will be at the 2019 Plant and Animal Genome (PAG) conference <https://galaxyproject.org/news/2019-01-galaxy-update/#galaxy-pag-2019> - Galaxy needs your Google Summer of Code Project suggestions <https://galaxyproject.org/news/2019-01-galaxy-update/#galaxy-needs-your-goo…> - And GalaxyAdmins needs your topic suggestions <https://galaxyproject.org/news/2019-01-galaxy-update/#galaxyadmins-needs-yo…> - 80 new publications <https://galaxyproject.org/news/2019-01-galaxy-update/#publications>, including several spectacular ones - Some most excellent Galaxy Platform News <https://galaxyproject.org/news/2019-01-galaxy-update/#galaxy-platforms-news>, including the *EGI Marketplace*. - The Contributor of the Month is ... Simon Gladman <https://galaxyproject.org/news/2019-01-galaxy-update/#new-galactic-blog-pos…> ! - 17 Open positions <https://galaxyproject.org/news/2019-01-galaxy-update/#whos-hiring> in 6 countries on 3 continents. - Doc, Hub, and Training Updates <https://galaxyproject.org/news/2019-01-galaxy-update/#doc-hub-and-training-…> covering RNA-Seq visualizations, BlockClust, cloud storage, cancer proteogenomics, and some introductory videos - ToolShed contributions <https://galaxyproject.org/news/2019-01-galaxy-update/#toolshed-contributions> - New releases <https://galaxyproject.org/news/2019-01-galaxy-update/#releases>: - Tripal Galaxy - connect Galaxy to your online database - BioBlend - a Python API for Galaxy and CloudMan - Planemo - utilities for building tools for Galaxy - And a bunch of other news <https://galaxyproject.org/news/2019-01-galaxy-update/#other-news> too See the newsletter for all of the details! Thanks for using Galaxy! Cheers, Mo Heydarian, on behalf of Galaxy

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End of 2018 Reminders: Admin Training, GCC2019 Training Topic Nominations, and GalaxyAdmins meetups topics
by Dave Clements 27 Dec '18

27 Dec '18

Happy Holidays all! A couple of reminders before 2019 arrives: - *Galaxy Admin Training <https://galaxyproject.org/events/2019-admin-training/>*, January 28-February 1. Learn best practices for installing and supporting your own Galaxy service. Split into a 2-day intro session, and a 3 day advanced session. *Advance registration ends December 31, and then rates go up by, um, a lot. Register by Monday.* - *GCC2019 Training Topic Nominations <https://galaxyproject.org/news/2018-12-gcc2019-training-nomination/> end 31 December! * Nominated topics will be voted on by the community in January. Topics nominated thus far are here <https://galaxyproject.org/events/gcc2019/training/#training-topic-nominatio…>. Please nominate new topics here <https://docs.google.com/forms/d/1fBPjEmw7Td52rhBnC0SvflnQCD7Ue5IMJ9RkM0SjnY…>, and if you want to expand on existing nominations <https://galaxyproject.org/events/gcc2019/training/#training-topic-nominatio…> you can edit the hub directly, or send the edits to me. (Note: I suspect, but don't know, that we'll extend this deadline into early January.) - *GalaxyAdmins meetups <https://galaxyproject.org/news/2018-12-galaxy-admins/>* will resume in 2019 <https://galaxyproject.org/news/2018-12-galaxy-admins/>. If you have ideas for meetup topics, please nominate them <https://docs.google.com/forms/d/e/1FAIpQLSfv257YcdQQO7gp3K4USoBzqkd-UDEblst…> . - We need your project ideas for *Google Summer of Code 2019* <https://docs.google.com/forms/d/e/1FAIpQLSfv257YcdQQO7gp3K4USoBzqkd-UDEblst…>*. *Please add your project ideas to the proposal, either directly on this page <http://gmod.org/wiki/GSOC_Project_Ideas_2019> (requires an account), of via this online form <http://bit.ly/gsoc-2019-ogi-propose>. Finally, for those of you not on Twitter, I can't resist sharing this post from Martin Čech <https://twitter.com/martenson?ref_src=twsrc%5Etfw%7Ctwcamp%5Eembeddedtimeli…> . See you in the new year, Dave C [image: 2018-12-26_12-01-57-martins-tree.png] -- https://galaxyproject.org/ https://usegalaxy.org/

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Galaxy Administrator Training, Jan 28 - Feb 1, Penn State University
by Dave Clements 21 Dec '18

21 Dec '18

Hello all, We are pleased to announce that* the 2019 Galaxy Admin Training <https://galaxyproject.org/events/2019-admin-training/> will be offered January 28 through February 1 at Penn State University* (where the Galaxy Project got started over ten years ago). The workshop offers a 2 day introductory session <https://github.com/galaxyproject/dagobah-training#basic-sessions> followed by a 3 day advanced topics session <https://github.com/galaxyproject/dagobah-training#advanced-sessions>. Participants can register for one or both sessions. This workshop will cover what you need to know to set up your own high-performance and multi-user production Galaxy instance. Sessions will be *intensive and hands-on*, and taught by experienced instructors from the Galaxy Community. Participants will learn how to install, configure, customize, and extend their own Galaxy servers. Topics include tool configuration, authentication and user management, using heterogeneous storage and compute services, and many other topics that will enable you to get your own Galaxy server up and running, performing well, and used by your community. Registration <https://galaxyproject.org/events/2019-admin-training/#registration> is now open and starts at $40 / day for participants from non-profits and academia. Early registration ends October 31. However, the 2016 and 2018 admin training were both full, so you are strongly encouraged to *register now*. *The workshop does have prerequisites <https://galaxyproject.org/events/2019-admin-training/#prerequisites>. Please read them before you register.* Cheers, Dave C. *About Galaxy * Galaxy is an open web based platform for biomedical data integration and analysis. It is deployed at large and small organizations around the world and used in a broad range of biomedical research domains, and across the tree of life. -- https://galaxyproject.org/ https://usegalaxy.org/

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tools gone after switching to galaxy.yml
by Matthias Bernt 20 Dec '18

20 Dec '18

Dear list, just tried to switch to galaxy.yml, which worked in general, but now tools that have been installed from the TS disappeared. In the logs I get for each tool: ``` galaxy.tools.toolbox.base ERROR 2018-12-19 13:28:15,815 [p:22877,w:0,m:0] [MainThread] Error reading tool from path: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/74a8bef53a00/text_pr… Traceback (most recent call last): File "lib/galaxy/tools/toolbox/base.py", line 563, in _load_tool_tag_set tool_shed_repository = self.get_tool_repository_from_xml_item(item, path) File "lib/galaxy/tools/toolbox/base.py", line 629, in get_tool_repository_from_xml_item raise Exception(msg) Exception: Attempted to load tool shed tool, but the repository with name 'text_processing' from owner 'bgruening' was not found in database ``` Any idea what could be wrong here? The connection to the DB seems to be functional, since I can see the users in the admin Panel. 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 -------------------------------------------

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Galaxy and Google Summer of Code 2019
by Dave Clements 19 Dec '18

19 Dec '18

Hello all, Galaxy will be applying to participate in the 2019 Google Summer of Code <https://summerofcode.withgoogle.com/>. We will again be participating as part of the *Open Genome Informatics Group <http://gmod.org/wiki/GSoC>* that also includes Bioconda <https://bioconda.github.io/>, GMOD <http://gmod.org/>, Reactome <https://reactome.org/>, MGI <http://www.informatics.jax.org/>, OICR <https://oicr.on.ca/research-portfolio/>, and WormBase <http://www.wormbase.org/>. We are currently building our group's proposal. If you have an idea for a project that you would be interested in mentoring someone for, then please add it to the proposal, either directly on this page <http://gmod.org/wiki/GSOC_Project_Ideas_2019> (requires an account), of via this online form <http://bit.ly/gsoc-2019-ogi-propose>. The deadline for submitting your projects is February 1. Thanks, Dave C "Google Summer of Code is a global program that offers student developers stipends to write code for various open source software projects. We work with many open source, free software, and technology-related groups to identify and fund projects over a three month period. Since its inception in 2005, the program has brought together over 14,000 successful student participants from 118 countries, 651 open source organizations, and over 35 million lines of code. Through Google Summer of Code, accepted student applicants are paired with a mentor or mentors from the participating projects, thus gaining exposure to real-world software development scenarios and the opportunity for employment in areas related to their academic pursuits. In turn, the participating projects are able to more easily identify and bring in new developers. Best of all, more source code is created and released for the use and benefit of all." -- https://galaxyproject.org/ https://usegalaxy.org/

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how to configure sub-uri in galaxy.yml
by Ping Luo 15 Dec '18

15 Dec '18

I am trying to configure Galaxy v18.09 wtih sub-uri. In prior 18.01, I use this configuration in conjunction with Apache rewrite rules and it works well: [filter:proxy-prefix] use = egg:PasteDeploy#prefix prefix = /msgalaxy [app:main] filter-with = proxy-prefix cookie_path = '/galaxy' In galaxy.yml, I know I need to uncomment and add the following filter-with: proxy-prefix cookie_path: '/galaxy' However, I don't know where and how to add filter:proxy-prefix. The comment in config.yml says: # If running behind a proxy server and Galaxy is served from a # subdirectory, enable the proxy-prefix filter and set the prefix in # the [filter:proxy-prefix] section above. which is for galaxy.ini file. An example on how to do it would be much appreciated. Ping

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Conda issue on a server using a sshfs mounting point
by Estelle Ancelet 13 Dec '18

13 Dec '18

Hi Galaxy team, I have a Galaxy server sharing a folder with a cluster through sshfs. The Galaxy folder is cloned on the cluster : /home/galaxy-user/galaxy. On the server, I have the same directory but empty : /home/galaxy-user/galaxy. On the server side, I use the following mounting command: sshfs -o cache=no galaxy-user@clusterfr:galaxy galaxy When I run galaxy (sh ./run.sh from galaxy-user in the VM), everything seems to go well but in fact, the _conda directory doesn’t contain any binary. It only contains the pkg folder. The log message I get is “cannot install conda because conda_prefix /home/galaxy-user/galaxy/database/dependencies/_conda exists and is not empty”. In the UI, if I try to install a tool with dependencies from the toolshed, I get the same log message. I’ve also tried sshfs -o cache=no,idmap=user,allow_other. But then, I cannot launch Galaxy. I have an arror (add error message). Any clue on how to make conda work with this infrastructure? Thanks in advance Estelle

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GalaxyAdmins is returning to a device near you in February 2019, and we need your help
by Dave Clements 13 Dec '18

13 Dec '18

Hi All After a two year hiatus, the bimonthly online GalaxyAdmins meetups <https://galaxyproject.org/community/galaxy-admins/meetups/> will return on February 28 <https://galaxyproject.org/community/galaxy-admins/meetups/2019-02-28/>. GalaxyAdmins <https://galaxyproject.org/community/galaxy-admins/> is a discussion group for Galaxy community members who are responsible for Galaxy installations. Our online meetups are around an hour long and feature a presentation followed by an open discussion. It's a great place to catch up on what your fellow admins are thinking about. *But, before we start meeting next year, we need to know what you care about <https://docs.google.com/forms/d/e/1FAIpQLSfv257YcdQQO7gp3K4USoBzqkd-UDEblst…>.* What do you want to learn? Who do you want to hear from? What's causing you trouble? Or, what have you worked that your fellow GalaxyAdmins would benefit from knowing? Got some ideas? *Nominate them <https://docs.google.com/forms/d/e/1FAIpQLSfv257YcdQQO7gp3K4USoBzqkd-UDEblst…>* We hope to see you in February, Helena Rasche <https://galaxyproject.org/people/helena-rasche/> and Dave Clements <https://galaxyproject.org/people/dave-clements/> -- https://galaxyproject.org/ https://usegalaxy.org/

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