- Small-scale-admins - lists.galaxyproject.org

Thursday, June 19th (3PM CEST) - next meeting of the "small scale servers" group
by Hans-Rudolf Hotz 20 Jun '25

20 Jun '25

Dear All Our next meeting will be this week on Thursday (June 19th) at 3PM CEST (1PM UTC) Please add any questions or topics you would like to discuss to our rolling minutes document: https://docs.google.com/document/d/1KTz4qxZBG4Z3sF23dVKPWXYz1mCNo2YDygSUHqt… Zoom link: https://unige.zoom.us/j/67916443799?pwd=ade4kVZgKinYAafDZnGKwomJM0ub0Q.1 Regards, Lucille and Hans-Rudolf PS: next meetings for your calendar: July 17th, 3PM CEST (1PM UTC) August 21st, 3PM CEST (1PM UTC) September 18th, 3PM CEST (1PM UTC) October 16th, 3PM CEST (1PM UTC)

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deploying Galaxy for the first time
by Juan Antonio Cordero Varela 17 Jun '25

17 Jun '25

Dear small scale Galaxy Admins, I am planning to deploy a production Galaxy Server to be used by the researchers at my research institute. I have been following the tutorials at Galaxy Training! <https://training.galaxyproject.org/training-material/learning-pathways/admi…> and some questions have come to mind: * *OS version*: Ubuntu 22.04 vs 24.04?: since the tutorial is a bit old already (based on Ubuntu 18.04), I assume I should stick to the latest stable Ubuntu version. * Should I install the *latest stable Galaxy* version (25.0 at this moment)? * Should Galaxy server be *on a VM or on a physical node*? My HPC infrastructure consists of login and management nodes working as VMs inside a Proxmox 7.X server, and a bunch of computing nodes (there's a couple dedicated storage nodes). If Galaxy and the PostgreSQL database are stored on the same VM and it has enough resources it would be quite easy to manage, since you can reboot it very quickly and it's possible and easy to take snapshots of the VM. * If the Galaxy Server is stored on a VM on the Proxmox host, I would not be able to access the VM directly from outside. Which changes should I make to access the Galaxy? Is there any alternative to redirect traffic to port 80 or 8080 from the Proxmox host to the VM? I’ve experienced some issues with Nginx if I do this, since Gunicorn uses a gunicorn.sock file instead. If I add iptables rules so that the proxmox server redirects all the traffic from its port 80 to the port 80 of the VM, I get the following error at nginx: |nginx: 2025/06/13 10:55:55 [crit] 46578#46578: *1 connect() to unix:/srv/galaxy/var/config/gunicorn.sock failed (2: No such file or directory) while connecting to upstream, client: 10.X.X.X, server: 192.168.2.X, request: "GET / HTTP/1.1", upstream: "http://unix:/srv/galaxy/var/config/gunicorn.sock:/", host: "10.X.X.X", referrer: "http://10.X.X.X/"| I've read I should use NGINX on the Proxmox host if I don't want to do port-forwarding with iptables. Alternatively the VPN from the research institute could be reconfigured or redirect directly to the VM. Do you have any thoughts about this? If this is not the right channel to ask, please let me know. Thanks a lot in advance, Cheers, Juan

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Thursday, May 15th (3PM CEST) - next meeting of the "small scale servers" group
by Hans-Rudolf Hotz 14 May '25

14 May '25

Dear All Our next meeting, will be on Thursday (May 15th) at 3PM CEST (1PM UTC) - back to our normal time slot! Please add any questions or topics you would like to discuss to our rolling minutes document: https://docs.google.com/document/d/1KTz4qxZBG4Z3sF23dVKPWXYz1mCNo2YDygSUHqt… Zoom link: https://unige.zoom.us/j/67916443799?pwd=ade4kVZgKinYAafDZnGKwomJM0ub0Q.1 Regards, Lucille and Hans-Rudolf PS: next meetings for your calendar: June 19th, 3PM CEST (1PM UTC) July 17th, 3PM CEST (1PM UTC) August 21st, 3PM CEST (1PM UTC) September 18th, 3PM CEST (1PM UTC) October 16th, 3PM CEST (1PM UTC) -- Hans-Rudolf Hotz, PhD Bioinformatics Support Friedrich Miescher Institute for Biomedical Research Fabrikstrasse 24 4056 Basel/Switzerland

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Thursday, April 17th (9AM CEST ! ) - next meeting of the "small scale servers" group
by Hans-Rudolf Hotz 14 Apr '25

14 Apr '25

Dear All Our next meeting, will be on Thursday (April 17th) at 9AM CEST (7AM UTC) - different time! and we have a new (permanent) zoom link: https://unige.zoom.us/j/67916443799?pwd=ade4kVZgKinYAafDZnGKwomJM0ub0Q.1 This time, we will be joined by Nuwan (https://training.galaxyproject.org/training-material/hall-of-fame/nuwang/) from the Galaxy Australia Team. He will talk about his experience with the TPV (Total Perspective Vortex, https://github.com/galaxyproject/total-perspective-vortex, https://total-perspective-vortex.readthedocs.io/en/latest/ ) Please add any questions you have for Nuwan to our rolling minutes document: https://docs.google.com/document/d/1KTz4qxZBG4Z3sF23dVKPWXYz1mCNo2YDygSUHqt… (obviously you can add any other topic you would like to discuss, as well) Regards, Lucille and Hans-Rudolf PS: next meetings for your calendar: May 15th, 3PM CEST (1PM UTC) June 19th, 3PM CEST (1PM UTC) July 17th, 3PM CEST (1PM UTC)

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Thursday, March 20th - next meeting of the "small scale servers" group
by Hans-Rudolf Hotz 14 Mar '25

14 Mar '25

Dear All Our next meeting, will be on Thursday (March 20th) at 3PM CET (2PM UTC) Please add any discussion points to our rolling minutes document: https://docs.google.com/document/d/1KTz4qxZBG4Z3sF23dVKPWXYz1mCNo2YDygSUHqt… zoom link (different link - just for March 20th): https://fmi.zoom.us/j/98449988704?pwd=rkOW2Kzhsd1RUm9alqCQdkzoMaxvqI.1 Regards, Lucille and Hans-Rudolf PS: next meetings for your calendar: April 17th, 9 AM CEST (7 AM UTC) - different time! (you should have received a new calendar invite) May 15th, 3PM CEST (1PM UTC) June 19th, 3PM CEST (1PM UTC) July 17th, 3PM CEST (1PM UTC) -- Hans-Rudolf Hotz, PhD Bioinformatics Support Friedrich Miescher Institute for Biomedical Research Fabrikstrasse 24 4056 Basel/Switzerland

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Updated invitation: small scale Galaxy Admins @ Thu Apr 17, 2025 9am - 10am (CEST) (small-scale-admins@lists.galaxyproject.org)
by Hans-Rudolf Hotz 14 Mar '25

14 Mar '25

This event has been updated Changed: time, description small scale Galaxy Admins Thursday Apr 17, 2025 ⋅ 9am – 10am Central European Time - Paris Minutes Guests emulatorer(a)gmail.com elsalatino(a)gmail.com m.vandenbeek(a)gmail.com ncoraor(a)gmail.com small-scale-admins(a)lists.galaxyproject.org View all guest info https://calendar.google.com/calendar/event?action=VIEW&eid=YzExZWttcHN1NzZu… Reply for small-scale-admins(a)lists.galaxyproject.org and view more details https://calendar.google.com/calendar/event?action=VIEW&eid=YzExZWttcHN1NzZu… Your attendance is optional. ~~//~~ Invitation from Google Calendar: https://calendar.google.com/calendar/ You are receiving this email because you are an attendee on the event. Forwarding this invitation could allow any recipient to send a response to the organizer, be added to the guest list, invite others regardless of their own invitation status, or modify your RSVP. Learn more https://support.google.com/calendar/answer/37135#forwarding

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Canceled event: small scale Galaxy Admins @ Thu Feb 20, 2025 9am - 10am (EST) (small-scale-admins@lists.galaxyproject.org)
by John Davis 21 Feb '25

21 Feb '25

This event has been canceled. small scale Galaxy Admins Thursday Feb 20, 2025 ⋅ 9am – 10am Eastern Time - New York MinutesZoom link Guests emulatorer(a)gmail.com elsalatino(a)gmail.com m.vandenbeek(a)gmail.com ncoraor(a)gmail.com small-scale-admins(a)lists.galaxyproject.org ~~//~~ Invitation from Google Calendar: https://calendar.google.com/calendar/ You are receiving this email because you are an attendee on the event. Forwarding this invitation could allow any recipient to send a response to the organizer, be added to the guest list, invite others regardless of their own invitation status, or modify your RSVP. Learn more https://support.google.com/calendar/answer/37135#forwarding

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Thursday, February 20th - next meeting of the "small scale servers" group
by Hans-Rudolf Hotz 14 Feb '25

14 Feb '25

Dear All Our next meeting, will be on Thursday (Feb 20th) at 3PM CET (2PM UTC) Please add any discussion points to our rolling minutes document: https://docs.google.com/document/d/1KTz4qxZBG4Z3sF23dVKPWXYz1mCNo2YDygSUHqt… zoom link: https://epfl.zoom.us/j/69775900853?pwd=R1gzbllUZzg0RFUrM0Mzd2MvczE3Zz09 Regards, Lucille and Hans-Rudolf PS: next meetings for your calendar: March 20th, 3PM CET (2PM UTC) April 17th, 3PM CET (1PM UTC) - TBC May 15th, 3PM CET (1PM UTC) -- Hans-Rudolf Hotz, PhD Bioinformatics Support Friedrich Miescher Institute for Biomedical Research Fabrikstrasse 24 4056 Basel/Switzerland

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Dynamic user ssh job submission
by VLAD VISAN 27 Jan '25

27 Jan '25

Hi all, Giuseppe, Lucille & Matthias were talking about submitting jobs to a cluster as the user launching the workflow, over ssh. Here is the summary of how we did it, by adding a "dynamic user" option to the existing cli.py runner (that can work over ssh) * Code modification: [ https://github.com/vladvisan/galaxy/commit/6276fd58d27d5b02035be0e16ae8641d… | https://github.com/vladvisan/galaxy/commit/6276fd58d27d5b02035be0e16ae8641d… ] * If you have any comments, I'm thinking of improving it and then submitting a PR ? * Our related related config: * use TPV * in tpv_rules_local.yml: * destinations: ssh_ord_mini: runner: cli params: shell_plugin: SecureShell shell_username: user-a#arbitrary, not actually used in dynamic mode job_partition: main * (comment which has no impact on the dynamic user aspect: we have no job_plugin k/v in "destinations" because we get let the user choose it step by step, using TPV) Hope it helps & appreciate any feedback as well, Regards, Vlad

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Thursday, January 16th - next meeting of the "small scale servers" group
by Hans-Rudolf Hotz 10 Jan '25

10 Jan '25

Dear All Happy New Year ! Our first meeting this year will be on Thursday (Jan 16th) at 3PM CET (2PM UTC) We already have several (left over from last year) discussion points. Nevertheless, feel free to add new ones to our rolling minutes document: https://docs.google.com/document/d/1KTz4qxZBG4Z3sF23dVKPWXYz1mCNo2YDygSUHqt… zoom link: https://epfl.zoom.us/j/69775900853?pwd=R1gzbllUZzg0RFUrM0Mzd2MvczE3Zz09 Regards, Lucille and Hans-Rudolf PS: next meetings for your calendar: February 20th, 3PM CET (2PM UTC) March 20th, 3PM CET (2PM UTC)

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