This is a bugfix for the future bug of missing documentation for 17.09 and before. 18.01 will require a significant rewrite of these pages for the uWSGI and configuration changes to Galaxy and the release_17.09 branch of these docs is now being hosted https://docs.galaxyproject.org/en/release_17.09/, so backporting this configuration documentation will allow us to provide permenant links to this 17.09 varaint of all this documentation (with information about paste and galaxy.ini for instance).
This content currently includes:
- the production configuration page
- the cluster configuration page
- the job configuration page
- the scaling information page
- the ftp configuration page
- the top-level nginx page (for external auth content still linking out to the hub)
- the top-level apache page (for external auth content still linking out to the hub)
- the job metrics configuration page
Includes small tweaks to sphinx documentation generation.
- Add a quick build mode that skips source generation / Python docs (export GALAXY_DOCS_SKIP_SOURCE=1 to build this way). This speeds up review of core Sphinx docs.
- Use AutoStructify for better Markdown integration.
Updates to the documentation above and beyond what is on the corresponding Hub pages to reflect more of the state of art as of 17.09 including:
- Update the job configuration page with information about XML macros.
- Mention and link to newer style resubmission condition expressions (not just an enumerated string anymore).
- Updated list of dynamic job runner configuration parameters.
- Mention the ``raw`` attribute for ``env`` directives in the job configuration page.
- Mention the ``total_walltime`` limit added in #3217.
- Drop mentions of older URL-based job conf configuration stuff.
- Mention newer Local and Paramiko based shell runners in CLI section.
- Mention newer slurm job styles in CLI section.
- Improved Pulsar links.
- Fix dataset security link in Apache display sites config.
- Update job metrics page to link to a new Github issue instead of old Trello issues.
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.
John Chilton