I pulled in this doc https://galaxyproject.org/develop/authentication/ which was very dated and somewhat incorrect and I filled it out with more details, updated configuration information, and a whole new section on the authentication framework. I also pulled in this doc https://galaxyproject.org/admin/user-accounts/ which was pretty good and I left it largely unchanged.
Rebased to fix index inclusion and with edits suggested by :eagle:👀.
1. Create a new API endpoint and client spin to wait for GIE containers to
become ready. IEs are not required to use it, but usage does require
a slight change to their `load_notebook()` functions.
2. Add a Docker swarm manager daemon that runs automatically
to add nodes when services are waiting, clean up exited services, and
remove idle nodes. Shuts down automatically when there's nothing to
do.
The format of the GIE proxy session database has changed, if GIEs are
running when you restart Galaxy, they will be interrupted. If you run
the GIE proxy separate from Galaxy, you should restart it after
upgrading.
- Add documentation for cached dependency management as solution to LOCKERRORS.
- Add documentation for overcoming problems with hard links. (Different approaches)
- Add documentation on upgrading Conda as needed.
- Correct and fill out documentation of defaults.
- Fix some bugs in the Galaxy packages documentation.
- Expand Galaxy package documentation to include a simpler example.
- Update Conda configuration option documentation to reflect new defaults.
- Update Conda configuration option documentation to discuss copy_dependencies.
- Cross link Conda and dependency resolver documentation as it makes sense.
- Add a link to the Bioconda channel order documentation for future reference.
- Make things a bit more concise in places - start with the implicit tl;dr.
not only for converting jupyter notebook to HTML (with nbconvert) but also
where ipython/IPython was referenced.
Some files still contain ipython but this is mostly related to documentation or
to the IE docker container itself.
E Rasche