Trouble Uploading Files to Local Galaxy v25 on Shared HPC

jennaj · September 5, 2025, 7:51pm

In the default configuration:

jobs are running on the host server (or proxy).

lib/galaxy/config/sample/job_conf.sample.yml

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          # Classes can be used to map groups of tools - the current classes include
          # - local (these special tools that aren't parameterized for remote execution - expression tools, upload, etc..)
          # - requires_galaxy (these special tools require Galaxy's Python environment during execution)
          # If a tool matches multiple classes, it will match the first class according to the order listed
          # above in this document (local, requires_galaxy).
          class: local
          environment: local

In short, the Upload jobs work a bit differently than the other tools and downloads are only about permissions. The instructions for configuring uploads can be found here → Production Environments — Galaxy Project 25.0.2.dev0 documentation

XRef → Private Galaxy Servers

Hope this helps and you can ask follow-up questions later on!