Hi Vlad, all,
https://github.com/usegalaxy-eu/shared-data was one attempt at uni-directional sync, yaml files describing data / URLs are kept continually in sync with target galaxies. Maybe not something very reusable but potentially useful as inspiration?
mvg
Helena
Hi Vlad,it was me who mentioned the library sync. I've heard of similar cases that Hans-Rudolf is describing and some more sophisticated ones that tried to do bi-directional sync. I couldn't find a link or any more information so I asked in one of the Galaxy channels -- maybe someone has a better memory (link). The thing is, that it is likely always going to be very custom and heavily based on what your other systems look like. Long time ago we had attempted to implement more full-featured LIMS in Galaxy, but that has long been gone since it was always just too general.Cheers,Martin_______________________________________________On Fri, Jul 19, 2024 at 3:03 PM VLAD VISAN <vlad.visan@univ-grenoble-alpes.fr> wrote:_______________________________________________Hi Hans, all,Thank you for sharing your solution.I've been looking into the API and have used this endpoint (strangely BioBlend seems to wrap around this less expressive one instead), very useful!If enough people have this synchronisation use-case, there could be a case for a Galaxy-provided link between a File Source (assuming your LIMS can be imported through one) and a Data Library.Regards,VladDe: "Hans-Rudolf Hotz" <hrh@fmi.ch>
À: "VLAD VISAN" <vlad.visan@univ-grenoble-alpes.fr>, "small-scale-admins" <small-scale-admins@lists.galaxyproject.org>
Envoyé: Vendredi 19 Juillet 2024 14:07:08
Objet: Re: [Small-scale-admins] Re: Today: Meeting of 'small scale servers' groupHi Vlad
> * I don't remember who mentioned a/several project(s) that synchronise
> data libraries with a given folder?
well, since I did not attend yesterday's meeting, I couldn't mention it...
In our case, all fastq files generated by our sequencing facility are
linked (not copied) to Data Libraries. There is a python script (running
every night) checking the facilitiy's LIMS for any new data. And then
based on the information in the LIMS, several calls to the Galaxy API
generate new sub-folders and link the data.
So it is a very customized solution fitting our local LIMS, storage
set-up, etc.
Regards, Hans-Rudolf
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