Arvados

Turns out I can't easily do this because we don't have a new playground instance to host stuff that the current instructions tell you to get from qr1hi.

15964-fix-docs is ready for a first look.

The original goal was to eliminate the references to qr1hi. This meant that it was blocked on the new playground being set up. I've since made sure that jutro and pirca should be set up properly to match the guide.

I also ended up going over a number of pages and reorganizing them for clarity, as well as deleting obsolete documentation.

The workbench sections still reference workbench 1, but I think updating it for Workbench 2 won't be so bad.

We also want to incorporate the big WGS demo/walkthrough that Sarah is working on, but that will be a different story.

Some comments:

• At file build/run-tests.sh line 1033 we’re still pointing to qr1hi to do the link checking. Not sure if this is being used, but worth mentioning it.
• At file lib/config/config.default.yml line 1287 we also reference qr1hi on an example URL. This gets included in the docs site.
• At file doc/user/getting_started/ssh-access-windows.html.textile.liquid
  • line 12 it says “…If you would like to use to access VM through your browser…” and might need some clarification.
  • “OS X” is called “macOS” since 2016 (in case you want to be picky about doc correctness 🙂)
• At file doc/user/tutorials/add-new-repository.html.textile.liquid line 12: typo “acess"
• The following files could be deleted, as it seems they aren’t being included anywhere.
  • doc/_includes/_0_filter_py.liquid
  • doc/_includes/_alert-incomplete.liquid
  • doc/_includes/_alert_stub.liquid
  • doc/_includes/_arv_copy_expectations.liquid
  • doc/_includes/_concurrent_hash_script_py.liquid
  • doc/_includes/_crunch1only_begin.liquid
  • doc/_includes/_crunch1only_end.liquid
  • doc/_includes/_example_docker.liquid
  • doc/_includes/_install_git.liquid
  • doc/_includes/_install_rails_reconfigure.liquid
  • doc/_includes/_install_ruby_and_bundler_sso.liquid
  • doc/_includes/_install_runit.liquid
  • doc/_includes/_pipeline_deprecation_notice.liquid
  • doc/_includes/_run_command_foreach_example.liquid
  • doc/_includes/_run_command_simple_example.liquid
  • doc/_includes/_run_md5sum_py.liquid
  • doc/_includes/_tutorial_bwa_sortsam_pipeline.liquid
  • doc/_includes/_tutorial_cluster_name.liquid
  • doc/_includes/_tutorial_hash_script_py.liquid
  • doc/_includes/_tutorial_submit_job.liquid
• At file doc/user/topics/arv-docker.html.textile.liquid the "x20vs" cluster references could be replaced with “zzzzz” for consistency with other examples.
• At file doc/_includes/_install_compute_docker.liquid line 9 there’s a mention of “pipeline” that might be confusing
• At file doc/user/getting_started/workbench.html.textile.liquid line 26 — the same as above.

I made all the changes suggested above

15964-fix-docs @ 8a41cc44ee196c9347785baa476a370abe77c75c

This LGTM, thanks!