September 2020 - galaxy-dev - lists.galaxyproject.org

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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