galaxy-dev

galaxy-dev@lists.galaxyproject.org

10006 discussions

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/

1 0

Re: [galaxy-bugs] Job running problems
by Jennifer Hillman-Jackson 25 Sep '20

25 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 > > >

1 0

Upgrade galaxy built from source?
by Sandra Maksimovic 23 Sep '20

23 Sep '20

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

2 1

September 2020 Galaxy Newsletter
by Dave Clements 02 Sep '20

02 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/

1 0

Gateways 2020 conference - of particular interest to Galaxy developers
by Katherine Lawrence 29 Aug '20

29 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.

1 0

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/

1 0

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

3 3

How to earn money online
by salihagenter＠gmail.com 16 Jul '20

16 Jul '20

Agenter is an Online Professional Networking Platform for Commission, where business profiles present their sales requirements on a commission basis and offer a new way of employment opportunities to the common people, sales agents, individuals to connect and earn a commission. With Agenter.com, anyone with interest can get a commission-based sales job from business profiles. Here you can find thousands of business profiles, providing commissions for the individual to increase their sales opportunity. So, the individual can make money online by working for the business. It benefits the individual who wants to earn a commission as a second income through this platform. The individual can approach the business for work which they can do and get paid. On the other hand, they can also refer the business to some other person who can finish the work and get the referral commission. Features And Benefits Of Agenter Include (For Individual Profiles) • Create your profile. (Free Sign Up) • Make connections with business profiles. • Find thousands of commission providers near you • Contact any business offering commission • Get your commission offers. • Start referring the business leads and get paid the agreed commissions Everyone is very passionate about getting jobs in their desired field. So, Agenter creates employment opportunities for everyone who can work as freelancers, agent and common people. Agenter is the best place for anyone who wants to earn more money online. Here you can make money in the form of commission by working for the business offers or referring them to the right individuals. You can also help others to make money online by referring the leads. To stand as an income opportunity generator for the global workforce. It is very easy anyone can work for any or multiple companies as their sales agent. To know more <a href="https://agenter.com/group/sales-jobs">sales executive</a> [url=https://agenter.com/group/sales-jobs]sales executive[/url] https://agenter.com/group/sales-jobs

1 0

***UNCHECKED*** A couple of BCC2020 Deadlines are today
by Dave Clements 11 Jul '20

11 Jul '20

Hi all, Just a reminder that there are a couple of BCC2020 (BOSC + Galaxy) deadlines today, July 10: 1. Birds of a feather submissions: https://bit.ly/bcc-propose-a-bof If you are attending the meeting part of BCC, and you would benefit from gathering your community at a BoF then please submit a proposal. We also need these. Right now we have lots of attendees, and very few BoFs (https://bcc2020.sched.com/overview/subject/BoF). This combination may not work well in an online setting. We might also extend the deadline to Sunday night. However, we might not. So if you see this today, then please submit in the next ~12 or so hours. 2. Early registration closes: https://bcc2020.github.io/Registration/ At US Pacific time. (about 13:45 from right now). Registration rates double after that, although they still aren't expensive. However, this event might sell out before the end of the day. So, might want to register now.... Thanks everyone, Dave C -- https://galaxyproject.org/

1 0

***UNCHECKED*** Nextflow within galaxy
by Luc Cornet 08 Jul '20

08 Jul '20

Hi everyone, I would like to run a Netxflow script in galaxy (yes I know it’s strange). So I made a test but I have a problem that I don’t undertstand, I am able to launch my Nextflow tool in galaxy but not to complete the analysis. The log out of galaxy : > juil.-07 19:28:53.888 [main] DEBUG nextflow.Session - Work-dir: /Users/luc/Documents/Programs/galaxy/database/jobs_directory/000/24/working/work [Mac OS X] juil.-07 19:28:53.888 [main] DEBUG nextflow.Session - Script base path does not exist or is not a directory: /Users/luc/Documents/Programs/galaxy/tools/BCCM-tools/bin juil.-07 19:28:53.988 [main] DEBUG nextflow.Session - Session start invoked juil.-07 19:28:54.296 [main] DEBUG nextflow.script.ScriptRunner - > Launching execution juil.-07 19:28:54.368 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null juil.-07 19:28:54.368 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' juil.-07 19:28:54.372 [main] DEBUG nextflow.executor.Executor - [warm up] executor > local juil.-07 19:28:54.375 [main] DEBUG n.processor.LocalPollingMonitor - Creating local task monitor for executor 'local' > cpus=4; memory=16 GB; capacity=4; pollInterval=100ms; dumpInterval=5m juil.-07 19:28:54.446 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > Testo -- maxForks: 4 juil.-07 19:28:54.477 [main] DEBUG nextflow.script.ScriptRunner - > Await termination juil.-07 19:28:54.477 [main] DEBUG nextflow.Session - Session await juil.-07 19:28:54.579 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run juil.-07 19:28:54.584 [Task submitter] INFO nextflow.Session - [37/23b693] Submitted process > Testo juil.-07 19:28:54.647 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 1; name: Testo; status: COMPLETED; exit: 0; error: -; workDir: /Users/luc/Documents/Programs/galaxy/database/jobs_directory/000/24/working/work/37/23b693d7b8dbbf227f19b3dd9780a7] juil.-07 19:28:54.674 [main] DEBUG nextflow.Session - Session await > all process finished juil.-07 19:28:54.675 [main] DEBUG nextflow.Session - Session await > all barriers passed juil.-07 19:28:54.682 [main] DEBUG nextflow.trace.StatsObserver - Workflow completed > WorkflowStats[succeedCount=1; failedCount=0; ignoredCount=0; cachedCount=0; succeedDuration=6ms; failedDuration=0ms; cachedDuration=0ms] juil.-07 19:28:54.855 [main] DEBUG nextflow.CacheDB - Closing CacheDB done juil.-07 19:28:54.869 [main] DEBUG nextflow.script.ScriptRunner - > Execution complete -- Goodbye And the log in galaxy: > juil.-08 11:38:09.834 [main] DEBUG nextflow.Session - Work-dir: /Users/luc/Documents/Programs/galaxy/database/jobs_directory/000/27/working/work [Mac OS X] juil.-08 11:38:09.834 [main] DEBUG nextflow.Session - Script base path does not exist or is not a directory: /Users/luc/Documents/Programs/galaxy/tools/BCCM-tools/bin juil.-08 11:38:10.001 [main] DEBUG nextflow.Session - Session start invoked juil.-08 11:38:10.373 [main] DEBUG nextflow.script.ScriptRunner - > Launching execution juil.-08 11:38:10.450 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null juil.-08 11:38:10.450 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' juil.-08 11:38:10.455 [main] DEBUG nextflow.executor.Executor - [warm up] executor > local juil.-08 11:38:10.458 [main] DEBUG n.processor.LocalPollingMonitor - Creating local task monitor for executor 'local' > cpus=4; memory=16 GB; capacity=4; pollInterval=100ms; dumpInterval=5m juil.-08 11:38:10.534 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > Testo -- maxForks: 4 juil.-08 11:38:10.591 [main] DEBUG nextflow.script.ScriptRunner - > Await termination Can someone help me with this ? Best, Luc ------------ Luc Cornet, PhD Bio-informatician Mycology and Aerobiology Sciensano

1 0

← Newer
1
...
5
6
7
8
9
10
11
...
1001
Older →

Jump to page:

2024

2023

2022

2021

2020

2019

2018

2017

2016

2015

2014

2013

2012

2011

2010

2009

2008

galaxy-dev