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Update more documentation for new config file, add 'group favorites'
[arvados.git] / doc / _config.yml
diff --git a/doc/_config.yml b/doc/_config.yml
index 2ac80f82881f858ecef4c25214e4b248ccef1486..814852fcc3c814792d63ea37cd9ecdcf3c254ac4 100644 (file)
--- a/doc/_config.yml
+++ b/doc/_config.yml
@@ -11,6 +11,8 @@
 # $ rake generate baseurl=/example arvados_api_host=example.com
 
 baseurl:
+current_version:
+all_versions:
 arvados_api_host: localhost
 arvados_cluster_uuid: local
 arvados_workbench_host: http://localhost
@@ -43,18 +45,19 @@ navbar:
       - user/topics/arv-copy.html.textile.liquid
       - user/topics/storage-classes.html.textile.liquid
       - user/topics/collection-versioning.html.textile.liquid
-    - Running workflows at the command line:
-      - user/cwl/cwl-runner.html.textile.liquid
-      - user/cwl/cwl-run-options.html.textile.liquid
     - Working with git repositories:
       - user/tutorials/add-new-repository.html.textile.liquid
       - user/tutorials/git-arvados-guide.html.textile.liquid
+    - Running workflows at the command line:
+      - user/cwl/cwl-runner.html.textile.liquid
+      - user/cwl/cwl-run-options.html.textile.liquid
     - Develop an Arvados workflow:
       - user/tutorials/intro-crunch.html.textile.liquid
       - user/tutorials/writing-cwl-workflow.html.textile.liquid
-      - user/cwl/federated-workflows.html.textile.liquid
       - user/cwl/cwl-style.html.textile.liquid
+      - user/cwl/federated-workflows.html.textile.liquid
       - user/cwl/cwl-extensions.html.textile.liquid
+      - user/cwl/cwl-versions.html.textile.liquid
       - user/topics/arv-docker.html.textile.liquid
     - Reference:
       - user/topics/link-accounts.html.textile.liquid
@@ -64,18 +67,6 @@ navbar:
       - user/copying/agpl-3.0.html
       - user/copying/LICENSE-2.0.html
       - user/copying/by-sa-3.0.html
-    - Obsolete documentation:
-      - user/topics/running-pipeline-command-line.html.textile.liquid
-      - user/topics/arv-run.html.textile.liquid
-      - user/tutorials/running-external-program.html.textile.liquid
-      - user/topics/crunch-tools-overview.html.textile.liquid
-      - user/tutorials/tutorial-firstscript.html.textile.liquid
-      - user/tutorials/tutorial-submit-job.html.textile.liquid
-      - user/topics/tutorial-parallel.html.textile.liquid
-      - user/topics/run-command.html.textile.liquid
-      - user/reference/job-pipeline-ref.html.textile.liquid
-      - user/examples/crunch-examples.html.textile.liquid
-      - user/topics/tutorial-trait-search.html.textile.liquid
   sdk:
     - Overview:
       - sdk/index.html.textile.liquid
@@ -86,7 +77,6 @@ navbar:
       - sdk/python/arvados-fuse.html.textile.liquid
       - sdk/python/events.html.textile.liquid
       - sdk/python/cookbook.html.textile.liquid
-      - sdk/python/crunch-utility-libraries.html.textile.liquid
     - CLI:
       - sdk/cli/install.html.textile.liquid
       - sdk/cli/index.html.textile.liquid
@@ -98,15 +88,19 @@ navbar:
     - R:
       - sdk/R/index.html.md
       - sdk/R/arvados/index.html.textile.liquid
-    - Perl:
-      - sdk/perl/index.html.textile.liquid
-      - sdk/perl/example.html.textile.liquid
     - Ruby:
       - sdk/ruby/index.html.textile.liquid
       - sdk/ruby/example.html.textile.liquid
-    - Java:
+    - Java v2:
+      - sdk/java-v2/index.html.textile.liquid
+      - sdk/java-v2/example.html.textile.liquid
+      - sdk/java-v2/javadoc.html.textile.liquid
+    - Java v1:
       - sdk/java/index.html.textile.liquid
       - sdk/java/example.html.textile.liquid
+    - Perl:
+      - sdk/perl/index.html.textile.liquid
+      - sdk/perl/example.html.textile.liquid
   api:
     - Concepts:
       - api/index.html.textile.liquid
@@ -120,6 +114,7 @@ navbar:
       - api/methods/authorized_keys.html.textile.liquid
       - api/methods/groups.html.textile.liquid
       - api/methods/users.html.textile.liquid
+      - api/methods/user_agreements.html.textile.liquid
     - System resources:
       - api/methods/keep_services.html.textile.liquid
       - api/methods/links.html.textile.liquid
@@ -134,13 +129,15 @@ navbar:
       - api/methods/container_requests.html.textile.liquid
       - api/methods/containers.html.textile.liquid
       - api/methods/workflows.html.textile.liquid
-    - Jobs engine (deprecated):
+    - Management (admin/system):
+      - api/dispatch.html.textile.liquid
+    - Jobs engine (legacy):
       - api/crunch-scripts.html.textile.liquid
       - api/methods/jobs.html.textile.liquid
       - api/methods/job_tasks.html.textile.liquid
       - api/methods/pipeline_instances.html.textile.liquid
       - api/methods/pipeline_templates.html.textile.liquid
-    - Metadata for bioinformatics:
+    - Metadata for bioinformatics (deprecated):
       - api/methods/humans.html.textile.liquid
       - api/methods/specimens.html.textile.liquid
       - api/methods/traits.html.textile.liquid
@@ -154,27 +151,35 @@ navbar:
   admin:
     - Topics:
       - admin/index.html.textile.liquid
-    - Upgrading and migrations:
-      - admin/upgrading.html.textile.liquid
-      - install/migrate-docker19.html.textile.liquid
-      - admin/upgrade-crunch2.html.textile.liquid
     - Users and Groups:
-      - install/cheat_sheet.html.textile.liquid
-      - admin/activation.html.textile.liquid
+      - admin/user-management.html.textile.liquid
+      - admin/reassign-ownership.html.textile.liquid
+      - admin/user-management-cli.html.textile.liquid
+      - admin/group-management.html.textile.liquid
+      - admin/federation.html.textile.liquid
       - admin/merge-remote-account.html.textile.liquid
       - admin/migrating-providers.html.textile.liquid
       - user/topics/arvados-sync-groups.html.textile.liquid
     - Monitoring:
-      - admin/health-checks.html.textile.liquid
+      - admin/logging.html.textile.liquid
       - admin/metrics.html.textile.liquid
+      - admin/health-checks.html.textile.liquid
       - admin/management-token.html.textile.liquid
-    - Cloud:
+    - Data Management:
+      - admin/favorites.html.textile.liquid
+      - admin/collection-versioning.html.textile.liquid
+      - admin/collection-managed-properties.html.textile.liquid
+      - admin/keep-balance.html.textile.liquid
+      - admin/controlling-container-reuse.html.textile.liquid
+      - admin/logs-table-management.html.textile.liquid
+      - admin/workbench2-vocabulary.html.textile.liquid
       - admin/storage-classes.html.textile.liquid
+    - Cloud:
       - admin/spot-instances.html.textile.liquid
+      - admin/cloudtest.html.textile.liquid
     - Other:
-      - admin/collection-versioning.html.textile.liquid
-      - admin/federation.html.textile.liquid
-      - admin/logs-table-management.html.textile.liquid
+      - install/migrate-docker19.html.textile.liquid
+      - admin/upgrade-crunch2.html.textile.liquid
   installguide:
     - Overview:
       - install/index.html.textile.liquid
@@ -184,11 +189,14 @@ navbar:
       - install/arvados-on-kubernetes.html.textile.liquid
     - Manual installation:
       - install/install-manual-prerequisites.html.textile.liquid
-      - install/install-components.html.textile.liquid
+      - install/packages.html.textile.liquid
+      - admin/upgrading.html.textile.liquid
+    - Configuration:
+      - install/config.html.textile.liquid
+      - admin/config-migration.html.textile.liquid
+      - admin/config.html.textile.liquid
     - Core:
-      - install/install-postgresql.html.textile.liquid
       - install/install-api-server.html.textile.liquid
-      - install/install-controller.html.textile.liquid
     - Keep:
       - install/install-keepstore.html.textile.liquid
       - install/configure-fs-storage.html.textile.liquid
@@ -198,23 +206,24 @@ navbar:
       - install/install-keep-web.html.textile.liquid
       - install/install-keep-balance.html.textile.liquid
     - User interface:
+      - install/setup-login.html.textile.liquid
       - install/install-sso.html.textile.liquid
       - install/install-workbench-app.html.textile.liquid
+      - install/install-workbench2-app.html.textile.liquid
       - install/install-composer.html.textile.liquid
     - Additional services:
       - install/install-ws.html.textile.liquid
-      - install/install-shell-server.html.textile.liquid
       - install/install-arv-git-httpd.html.textile.liquid
-    - Containers API support on SLURM:
-      - install/crunch2-slurm/install-prerequisites.html.textile.liquid
-      - install/crunch2-slurm/install-slurm.html.textile.liquid
+      - install/install-shell-server.html.textile.liquid
+    - Containers API:
       - install/crunch2-slurm/install-compute-node.html.textile.liquid
+      - install/install-jobs-image.html.textile.liquid
+      - install/install-dispatch-cloud.html.textile.liquid
       - install/crunch2-slurm/install-dispatch.html.textile.liquid
       - install/crunch2-slurm/install-test.html.textile.liquid
-      - install/install-nodemanager.html.textile.liquid
-      - install/install-compute-ping.html.textile.liquid
-    - Containers API support on cloud (experimental):
-      - install/install-dispatch-cloud.html.textile.liquid
-    - Jobs API support (deprecated):
-      - install/install-crunch-dispatch.html.textile.liquid
-      - install/install-compute-node.html.textile.liquid
+    - External dependencies:
+      - install/install-postgresql.html.textile.liquid
+      - install/ruby.html.textile.liquid
+      - install/nginx.html.textile.liquid
+      - install/google-auth.html.textile.liquid
+      - install/install-docker.html.textile.liquid