NeLS Connections in usegalaxy - usegalaxy-no/galaxyadmin GitHub Wiki

How is usegalaxy configured to use nels?

Connections to nels are used for nels oidc login and also to get data from nels.

Nels login oidc

The nels oidc is configured using the config tag oidc_backends_config_file in the galaxy.yml config file to ref the file /srv/galaxy/config/oidc_backends.xml This xml files look like this:

    <provider name="NeLS">
        <client_id>usegalaxy-test</client_id>
        <client_secret>********</client_secret>
        <redirect_uri>https://test.usegalaxy.no/authnz/nels/callback</redirect_uri>
        <icon>https://test.usegalaxy.no/static/images/feide_or_nels.svg</icon>
        <prompt>consent</prompt>
    </provider>
</OIDC>

Searching the infrastructure playbook repo also release that we are souring code direcly frome nels.bioinfo.no for styling of the website.

Nels Storage Plugin:

The configuration for the nels storage plugin can be found her: /srv/galaxy/server/tool-data/nels_storage_config.loc

[Parameters]
API_URL=https://test-fe.cbu.uib.no/nels-storage2
CLIENT_KEY=usegalaxy_no_test
CLIENT_SECRET=******

We also have this file /srv/galaxy/config/file_sources_conf.yml that spesifies wher the personal files and porject files are in nels.

- type: nels
  id: nels_storage_personal
  label: "NeLS Storage"
  doc: "Your personal folder in NeLS Storage"
  nels_config: "/srv/galaxy/server/tool-data/nels_storage_config.loc"
  writable: true
  userid: ${user.email}
  homedir: "/nels/users/<user>/Personal"
  ignore_hidden: true

- type: nels
  id: nels_storage_projects
  label: "NeLS Storage Projects"
  doc: "Your projects folder in NeLS Storage"
  nels_config: "/srv/galaxy/server/tool-data/nels_storage_config.loc"
  writable: true
  userid: ${user.email}
  homedir: "/nels/users/<user>/Projects"
  ignore_hidden: true

The nels py code is under /srv/galaxy/server/lib/galaxy/files/sources/nels.py

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