galaxy-dev July 2020

galaxy-dev@lists.galaxyproject.org

6 participants
6 discussions

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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***UNCHECKED*** A couple of BCC2020 Deadlines are today
by Dave Clements 10 Jul '20

10 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/

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***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

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July Galaxy News: BCC2020 Deadlines, Schedule, Fellowships; Galaxy Dev Roundtable, ...
by Dave Clements 01 Jul '20

01 Jul '20

The July 2020 Galaxy News is here: https://galaxyproject.org/news/2020-07-galaxy-update/ In the July 2020 Issue * BCC2020 starts July 17 * Early registration ends July 10 * BoF proposals due July 10 * Fellowships due July 5 * New Silver Sponsor: GalaxyWorks * Full training, talk, and poster/demo schedules are online * Galaxy and the NCBI Sequence Read Archive (SRA) * Upcoming events * Including the new Galaxy Developer Roundtable * Galaxy Platform News * Training material and doc updates * Who's Hiring * New blog posts * New Releases See you online in just over 2 weeks, Dave C -- https://galaxyproject.org/

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galaxy-dev July 2020