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

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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Thursday, December 19th - next meeting of the "small scale servers" group
by Hans-Rudolf Hotz 13 Dec '24

13 Dec '24

Dear All After changing our meeting schedule to once a month, the small scale admins will meet for another meeting this year, on Thursday (Dec 19th) at 3PM CET (2PM UTC) As a 'treat' for the festive season, we will have a special guest: Björn Grüning will 'enlighten' us about the use of 'User Object Store at usegalaxy.eu'. rolling minutes: 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: January 16th, 3PM CET (2PM UTC) February 20th, 3PM CET (2PM UTC) March 20th, 3PM CET (2PM UTC) -- Hans-Rudolf Hotz, PhD Bioinformatics Support Friedrich Miescher Institute for Biomedical Research Fabrikstrasse 24 4056 Basel/Switzerland

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Small follow-up recent meeting
by VLAD VISAN 26 Nov '24

26 Nov '24

Hi all, As promised, a small follow-up: Custom Object Store I presented : * added a few comments to the sheet, but the notes were already very thorough, thank you! * I didn't think it useful to add the slides and diagrams, but if you want them feel free to reach out! Data Library delay : * I couldn't find an existing issue -> created an [ https://github.com/galaxyproject/galaxy/issues/19209 | issue detailing it & possible solutions ] Thanks again for your feedback, Regards, Vlad

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the next meeting of the "small scale servers" group will already take place in December
by Hans-Rudolf Hotz 25 Nov '24

25 Nov '24

Dear All At our last meeting (see the rolling minutes: https://docs.google.com/document/d/1KTz4qxZBG4Z3sF23dVKPWXYz1mCNo2YDygSUHqt…) we decided to switch to a monthly schedule. Hence, our next meeting will already be on Thursday, December 19th at 3PM CET (2PM UTC) We will update the google "GalaxyWG" calendar accordingly. Regards, Lucille and Hans-Rudolf PS: next meetings for your calendar: January 16th, 3PM CET (2PM UTC) February 20th, 3PM CET (2PM UTC) March 20th, 3PM CET (2PM UTC) -- Hans-Rudolf Hotz, PhD Bioinformatics Support Friedrich Miescher Institute for Biomedical Research Fabrikstrasse 24 4056 Basel/Switzerland

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Updated invitation with note: small scale Galaxy Admins @ Monthly from 3pm to 4pm on the third Thursday 12 times (CET) (small-scale-admins@lists.galaxyproject.org)
by Hans-Rudolf Hotz 25 Nov '24

25 Nov '24

This event has been updated with a note: "we switch to monthly meetings Regards, Hans-Rudolf" Changed: time, location, description small scale Galaxy Admins Monthly from 3pm to 4pm on the third Thursday 12 times Central European Time - Paris 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 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. To stop receiving future updates for this event, decline this 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, November 21st - next meeting of the "small scale servers" group
by Hans-Rudolf Hotz 18 Nov '24

18 Nov '24

Dear All Our next meeting, will be on Thursday, November 21st at 3PM CET (2PM UTC) zoom link: https://fmi.zoom.us/j/98073380544?pwd=NnRFemhtWUJFeEhvRU5Wbk5TKzY5QT09 We have already a pretty interesting list of topics to discuss: https://docs.google.com/document/d/1KTz4qxZBG4Z3sF23dVKPWXYz1mCNo2YDygSUHqt… Regards, Lucille and Hans-Rudolf PS: next meetings for your calendar: January 16th, 3PM CET (2PM UTC) March 20th, 3PM CET (2PM UTC) -- Hans-Rudolf Hotz, PhD Bioinformatics Support Friedrich Miescher Institute for Biomedical Research Fabrikstrasse 24 4056 Basel/Switzerland

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Follow-up 19 Sept SSA meeting
by VLAD VISAN 25 Sep '24

25 Sep '24

Hi all, Thank you (to Lucille I think) for the [ https://docs.google.com/document/d/1KTz4qxZBG4Z3sF23dVKPWXYz1mCNo2YDygSUHqt… | detailed note-taking ] for the last meeting. I was able to catch up & had a few short comments/questions Conda : * Thanks for the information, I informed my team * I've not used conda in Galaxy, so my suggestions might be off, but * maybe make sure that a user cannot somehow override the conda-forge channel (through tool XML or other). * Maybe even consider IP/URL blocking any official conda links? NFS Object Store * I use NFS mounting on my Galaxy instance too (for an Object Source, and for Data Libraries) * Once the NFS folder/partition is mounted, it can be used as a regular folder? (transparent for Galaxy) * So I'm wondering why the need for the plugin in Galaxy? * Does your use-case mandate an Object Store and not a File Source? * I see a [ https://github.com/galaxyproject/galaxy/blob/9524be3b7ac0a0656aedd7596fb87a… | sshfs File Source ] already exists and that [ https://blog.ja-ke.tech/2019/08/27/nas-performance-sshfs-nfs-smb.html | sshfs is becoming competitive with NFS ] Interactive Tools * Very cool, thanks! * We have some Jupyter Notebook users locally (not (yet) in Galaxy), this could be useful to them. Scratch Object Stores, & per-user Object Stores : * If I'm not mistaken, these are both features mentioned in the recent GCC? * Do you know when the videos/slides will be available for this GCC? ( I just checked [ https://www.youtube.com/@GalaxyProject/videos | https://www.youtube.com/@GalaxyProject/videos ] ) Thank you, Vlad

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