X-Git-Url: https://git.arvados.org/arvados.git/blobdiff_plain/4aa3a732cac495fb384a521b2046f6b7f09dd13d..3aaefcb3c76ff470b475d950398d01255e87712a:/doc/_config.yml

diff --git a/doc/_config.yml b/doc/_config.yml
index 36e8c64b86..5386e8797a 100644
--- a/doc/_config.yml
+++ b/doc/_config.yml
@@ -24,40 +24,41 @@ navbar:
     - Welcome:
       - user/index.html.textile.liquid
       - user/getting_started/community.html.textile.liquid
+    - Walkthough:
+      - user/tutorials/wgs-tutorial.html.textile.liquid
     - Run a workflow using Workbench:
       - user/getting_started/workbench.html.textile.liquid
       - user/tutorials/tutorial-workflow-workbench.html.textile.liquid
-      - user/composer/composer.html.textile.liquid
+    - Working at the Command Line:
+      - user/getting_started/setup-cli.html.textile.liquid
+      - user/reference/api-tokens.html.textile.liquid
+      - user/getting_started/check-environment.html.textile.liquid
     - Access an Arvados virtual machine:
       - user/getting_started/vm-login-with-webshell.html.textile.liquid
       - user/getting_started/ssh-access-unix.html.textile.liquid
       - user/getting_started/ssh-access-windows.html.textile.liquid
-      - user/getting_started/check-environment.html.textile.liquid
-      - user/reference/api-tokens.html.textile.liquid
     - Working with data sets:
       - user/tutorials/tutorial-keep.html.textile.liquid
       - user/tutorials/tutorial-keep-get.html.textile.liquid
       - user/tutorials/tutorial-keep-mount-gnu-linux.html.textile.liquid
       - user/tutorials/tutorial-keep-mount-os-x.html.textile.liquid
       - user/tutorials/tutorial-keep-mount-windows.html.textile.liquid
-      - user/topics/keep.html.textile.liquid
       - user/tutorials/tutorial-keep-collection-lifecycle.html.textile.liquid
       - 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/topics/storage-classes.html.textile.liquid
+    - Data Analysis with Workflows:
       - 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
-    - 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/topics/arv-docker.html.textile.liquid
       - user/cwl/cwl-style.html.textile.liquid
       - user/cwl/cwl-extensions.html.textile.liquid
-      - user/topics/arv-docker.html.textile.liquid
+      - user/cwl/federated-workflows.html.textile.liquid
+      - user/cwl/cwl-versions.html.textile.liquid
+    - Working with git repositories:
+      - user/tutorials/add-new-repository.html.textile.liquid
+      - user/tutorials/git-arvados-guide.html.textile.liquid
     - Reference:
       - user/topics/link-accounts.html.textile.liquid
       - user/reference/cookbook.html.textile.liquid
@@ -66,18 +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
@@ -86,9 +75,9 @@ navbar:
       - sdk/python/example.html.textile.liquid
       - sdk/python/python.html.textile.liquid
       - sdk/python/arvados-fuse.html.textile.liquid
-      - sdk/python/events.html.textile.liquid
+      - sdk/python/arvados-cwl-runner.html.textile.liquid
       - sdk/python/cookbook.html.textile.liquid
-      - sdk/python/crunch-utility-libraries.html.textile.liquid
+      - sdk/python/events.html.textile.liquid
     - CLI:
       - sdk/cli/install.html.textile.liquid
       - sdk/cli/index.html.textile.liquid
@@ -100,9 +89,6 @@ 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
@@ -113,6 +99,9 @@ navbar:
     - 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
@@ -126,6 +115,7 @@ 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
@@ -134,74 +124,102 @@ navbar:
       - api/methods/virtual_machines.html.textile.liquid
       - api/methods/keep_disks.html.textile.liquid
     - Data management:
+      - api/keep-webdav.html.textile.liquid
+      - api/keep-s3.html.textile.liquid
+      - api/keep-web-urls.html.textile.liquid
       - api/methods/collections.html.textile.liquid
       - api/methods/repositories.html.textile.liquid
     - Container engine:
       - 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
   architecture:
     - Topics:
       - architecture/index.html.textile.liquid
-      - api/storage.html.textile.liquid
+    - Storage in Keep:
+      - architecture/storage.html.textile.liquid
+      - architecture/keep-clients.html.textile.liquid
+      - architecture/keep-data-lifecycle.html.textile.liquid
+      - architecture/manifest-format.html.textile.liquid
+    - Computation with Crunch:
       - api/execution.html.textile.liquid
+    - Other:
       - api/permission-model.html.textile.liquid
       - architecture/federation.html.textile.liquid
   admin:
     - Topics:
       - admin/index.html.textile.liquid
-    - Configuration:
-      - admin/config.html.textile.liquid
-    - Upgrading and migrations:
-      - admin/upgrading.html.textile.liquid
-      - admin/config-migration.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/user-management-cli.html.textile.liquid
+      - admin/reassign-ownership.html.textile.liquid
+      - admin/link-accounts.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
+      - admin/scoped-tokens.html.textile.liquid
+      - admin/token-expiration-policy.html.textile.liquid
+      - admin/user-activity.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:
-      - admin/storage-classes.html.textile.liquid
-      - admin/spot-instances.html.textile.liquid
-      - admin/cloudtest.html.textile.liquid
     - Data Management:
       - admin/collection-versioning.html.textile.liquid
       - admin/collection-managed-properties.html.textile.liquid
-    - Other:
-      - admin/federation.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
+      - admin/keep-recovering-data.html.textile.liquid
+    - Cloud:
+      - admin/spot-instances.html.textile.liquid
+      - admin/cloudtest.html.textile.liquid
+    - Other:
+      - install/migrate-docker19.html.textile.liquid
+      - admin/upgrade-crunch2.html.textile.liquid
   installguide:
     - Overview:
       - install/index.html.textile.liquid
     - Docker quick start:
       - install/arvbox.html.textile.liquid
+    - Installation with Salt:
+      - install/salt.html.textile.liquid
+      - install/salt-vagrant.html.textile.liquid
+      - install/salt-single-host.html.textile.liquid
+      - install/salt-multi-host.html.textile.liquid
     - Arvados on Kubernetes:
       - install/arvados-on-kubernetes.html.textile.liquid
+      - install/arvados-on-kubernetes-minikube.html.textile.liquid
+      - install/arvados-on-kubernetes-GKE.html.textile.liquid
+    - Automatic installation:
+      - install/automatic.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
@@ -211,23 +229,24 @@ navbar:
       - install/install-keep-web.html.textile.liquid
       - install/install-keep-balance.html.textile.liquid
     - User interface:
-      - install/install-sso.html.textile.liquid
+      - install/setup-login.html.textile.liquid
+      - install/install-ws.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-webshell.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
+    - Containers API:
+      - install/install-jobs-image.html.textile.liquid
+      - install/crunch2-cloud/install-compute-node.html.textile.liquid
+      - install/crunch2-cloud/install-dispatch-cloud.html.textile.liquid
       - install/crunch2-slurm/install-compute-node.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/install-docker.html.textile.liquid