- galaxy-dev - lists.galaxyproject.org

Galaxy Paper Cuts Day: Wednesday October 19
by Dave Clements 20 Oct '20

20 Oct '20

Hi all, We are organising the Galaxy Paper Cuts contribution fest this Wednesday*: https://galaxyproject.org/events/2020-10-papercuts/ Paper Cuts are small irritants that introduce friction when using or administering Galaxy. We want to 1) get rid of them, thus improving Galaxy 2) grow the contributor community! Want to help / learn / join? Please sign up. (You can also just show up, but then you won't get a reminder email.) Between now and the end of Wednesday, there are a couple of big ways you can help: 1. Participate! 2. Create GitHub issues for things that you find irritating, in any part of the Galaxy ecosystem 3. If you manage a Galaxy component (e.g., BioBlend, Planemo, ...) create a tag for paper cuts, tag any appropriate issues with it, and then let us know what tag you used.** Hope to see you on Wednesday, Dave C channeling Simon, Björn, and Dannon (in time zone order!) * This Wednesday == 21 hours from now in Australia ** Or just update the paper cuts page in the hub directly. -- https://galaxyproject.org/

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Segmentation fault
by James White 09 Oct '20

09 Oct '20

We have installed Galaxy on a local server with these os and programs: CentOS Linux release 8.1.1911 galaxy release_20.09 Python 3.6.8 When we configured object store for disk store it worked fine. We tried to configure Google Compute Platform and followed the instructions to create a bucket and install the .json key. When we test it it starts for a short time and then fails. /lib64/libpython3.6m.so.1.0(+0x1cd274) [0x7f1f5d9da274] /lib64/libpthread.so.0(+0x82de) [0x7f1f5d5f52de] /lib64/libc.so.6(clone+0x43) [0x7f1f5cb9ce83] *** end of backtrace *** run.sh: line 91: 18100 Segmentation fault (core dumped) .venv/bin/uwsgi --yaml /usr/local/galaxy/config/galaxy.yml --static-safe /usr/local/galaxy/client/src/assets Will appreciate any suggestions. Jim W -- Programmer Dept. of Entomology and Plant Pathology N.C. State Univ. Raleigh, N.C.

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October Galaxy Newsletter
by Dave Clements 07 Oct '20

07 Oct '20

Hello all, The October Galaxy Newsletter is out. https://galaxyproject.org/news/2020-10-galaxy-update/ News on * Event news & JTech Scholarships * Galaxy platform news: BRIDGE, BioCompute Object, French Galaxies, PhagePromoter, and UseGalaxy.* * Blog posts: Remote training, EOSC-Life calls * Training material and doc updates: refgenie magic * Publications * Q: Who's hiring? A: Ten different groups * New releases * Other news too If you have anything to include to next month's newsletter, then please send it to outreach(a)galaxyproject.org. Thanks, Dave C and Bea ________________________________ -- https://galaxyproject.org/

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Re: [galaxy-bugs] Job running problems
by Jennifer Hillman-Jackson 24 Sep '20

24 Sep '20

Hi David, If you are running the work at a public Galaxy server, the queue times for larger compute-intensive tools are usually a bit longer than for simpler tools. The best strategy is to queue jobs up and allow those to fully process. If you delete and rerun, that will place the new job back at the end of the queue again, further extending wait time. The only reason to rerun is if you already know there is a problem with the inputs that will likely lead to a job failure (or results you don't want). For urgent or time-sensitive work, or if you'd just like to have more quota space and not compete with others for common public resources, consider setting up your own Galaxy server. The GVL version of Cloudman is a popular choice but there are many others. Please see: https://galaxyproject.org/use/ Best, Jen -- Jennifer Hillman-Jackson Galaxy Application Support https://usegalaxy.org https://galaxyproject.org https://galaxyproject.org/support https://galaxyproject.org/learn https://help.galaxyproject.org On Mon, Aug 3, 2020 at 10:47 AM Xiaoshen Zhang <xiaoshen_zhang(a)tongji.edu.cn> wrote: > Dear Galaxy team, > > Recently, I have been running TRINITY for RNA-seq data analysis, but the > “my history” status always display the job is waiting to be run (the color > never changed). When I implemented some analyses on galaxy, ONLY this > method displayed “job waiting to be run” and nothing happened. > > After trying for several times and everything, I suppose something wrong > with my account or the TRINITY method. > > Hope you can kindly fix this problem. Thanks for all the efforts you have > been made. My account is exactly this email address. > Details for TRINITY: ( > https://usegalaxy.org/root?tool_id=toolshed.g2.bx.psu.edu/repos/iuc/trinity… > ) > > Best Regard, > > David > > >

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Upgrade galaxy built from source?
by Sandra Maksimovic 22 Sep '20

22 Sep '20

Hi there, Does anyone know of a best practice method to upgrade a Galaxy instance built from source? Thanks, Sandra

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September 2020 Galaxy Newsletter
by Dave Clements 01 Sep '20

01 Sep '20

Hello all, After a one month hiatus, the monthly Galaxy newsletter (https://galaxyproject.org/news/2020-09-galaxy-update/) is back (and there is a lot going on): * BCC2020 wrap up, and GCC2021 is on the way * More event news (some this week) * Galaxy platform news on * UseGalaxy.fr (!), ML Workbench, deepTS, BioCompute Object, and PiRATE * Blog posts * GVL Bets, SARS-CoV-2 (x2), climate science, get your tool in Galaxy, and Galaxy hits 10K pubs * Training material and doc updates (13 new and updated) * Publications (19 highlighted, 671 total) * Who's hiring * Institut Pasteur, UConn, Johns Hopkins, BSC, VIB & NCBI * New releases of Nebulizer and BioBlend * And other news too If you have anything to include in next month's newsletter, then please send it to outreach(a)galaxyproject.org. Cheers, Dave C -- https://bcc2020.github.io/ https://galaxyproject.org/

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Gateways 2020 conference - of particular interest to Galaxy developers
by Katherine Lawrence 28 Aug '20

28 Aug '20

This conference may be of interest to anyone who is building portals or web-based tools to improve access to specialized computing resources for a research or education community. The conference is online this year, and it costs just $100 ($50 for students), with registration support available to those with frozen discretionary funds. Happy to answer any questions you may have! --Katherine *Gateways 2020* /Virtual experience. Real takeaways. / <https://sciencegateways.org/gateways2020>https://sciencegateways.org/gateways2020 We get it. Your time is precious, and your attention is limited, but staying on top of the latest opportunities in gateways matters more than ever in today’s virtual world. Gateways 2020 has been redesigned to efficiently bring you rich content and distributed connections, just like gateways do. We’ve crafted a simple schedule, spread over two weeks, so you can learn, share, connect, and still have time to cook dinner. /What you’ll get:/ * Plenary events featuring experienced gateway creators and savvy scientists from whom you can *learn best practices* * Concurrent sessions that dig into the content with interactive discussions from which you can *synthesize new ideas* * Learning Labs on important topics that emerge during the conference where you may *establish new collaborations* * Choose up to four out of eight tutorials and workshops where you can *gain in-depth expertise* on specific topics * Opportunities to grow your network by *meeting people who can make a difference* to your gateway /Join us!/Registration is now open at https://sciencegateways.org/register2020until *Monday,* *October 5.* / Anyone is welcome to participate in the Poster Showcase. /The deadline to submit an abstract for your poster is *Friday, September 11:* <https://sciencegateways.org/web/gateways2020/program/poster>https://sciencegateways.org//web/gateways2020/program/poster. / Are travel expenses a concern for you?/Registration Support Grants are available to those who have frozen or otherwise unavailable funds. *Apply by Friday, October 2:* <https://sciencegateways.org/web/gateways2020/attend/support>https://sciencegateways.org/web/gateways2020/attend/support. * Gateways 2020 volunteers needed!* Are you a Zoom ninja? Do you have a good kitchen timer? Can you ask good questions? Gateways 2020 needs reliable volunteers to staff the help desk and host or moderate sessions. If this makes you smile, let us know. Email <mailto:help@sciencegateways.org>help(a)sciencegateways.org <mailto:help@sciencegateways.org>. * Cloudify Your Gateway!* Submit a proposal for Cloudify Gateways 2020. Adapt your gateway to use Google Cloud Platform and CloudyCluster, a parallel computation resource. Through the solicitation, you can get credits and, more importantly, support time for using cloud services. *Deadline: Friday, September 4.* Learn more at <https://sciencegateways.org/cloudify2020>https://sciencegateways.org/cloudify2020.

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Galaxy Interactive Tools - linked to wrong port
by Doris Brockmann 28 Jul '20

28 Jul '20

Hi, I installed Galaxy on an Ubuntu (18.04) VM following the 'Galaxy Installation with Ansible' tutorial. Galaxy is serving on localhost and does not use SSL. I then followed the 'Galaxy Interactive Tools' tutorial to install/enable Interactive Tools. I skipped the part 'Getting a wildcard SSL certificate' and I modified the group variables file group_vars/galayservers.yml as follows nginx_servers: - galaxy # NOT redirect-ssl - galaxy-gie-proxy instead of nginx_ssl_servers: - galaxy - galaxy-gie-proxy and in the templates/nginx/galaxy-gie-proxy.j2 file, I changed server { # Listen on port 443 listen *:443 ssl; to server { # Listen on port 80 (no SSL) listen *:80; When I execute EtherCalc (or RStudio), the link given in the blue box under 'click here to display' is something like this: http://4b187121143038ff-e0f2473dafce49c98787ab723e8a39b1.interactivetoolent… but the actual view is found here (modification by hand): http://4b187121143038ff-e0f2473dafce49c98787ab723e8a39b1.interactivetoolent… It seems that the Interactive Tools Proxy serves on the wrong port. The gie_proxy_port is 8000 and the proxy_pass in /etc/nginx/sites-enabled/galaxy-gie-proxy is http://localhost:8000 Does anyone have an idea how to solve the problem? Thanks in advance, Doris -- Doris BROCKMANN *INRAE Transfert BU* 60 Rue Nicolas Leblanc, 11100 Narbonne, France doris.brockmann(a)inrae.fr Tel. : +33 (0)4 68 46 64 32 Portable : +33 (0)6 03 18 97 76 *Visitez nos sites web**: *www.montpellier.inra.fr/it-e <http://www.montpellier.inra.fr/it-e> // /INRAE Transfert - Filiale de l'INRA - Siège social : 28, rue du Dr Finlay - 75015 Paris// //Société par actions simplifiée au capital de 1 920 000 € - RCS PARIS B 433 960 762 SIRET : 433 960 762 00030 – APE 671 C – TVA FR 96 433 960 762/

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To implement a one-click test for a Galaxy tool.
by Jin Li 16 Jul '20

16 Jul '20

Hi all, We have a tool in Galaxy at https://usegalaxy.eu/root?tool_id=moabs. We want to implement a one-click test using small data so that users can quickly understand how to use the interface. There are two difficulties in implementing the one-click test. 1. How to store small test data so that every new user can access it? 2. How to configure program settings automatically for the test data? so that the test data is automatically uploaded, and other parameters are pre-configured. Please help suggest any possible solution to a one-click test. Thank you. Best regards, Jin

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by salihagenter＠gmail.com 16 Jul '20

16 Jul '20

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