doc/_config.yml

   1 # Copyright (C) The Arvados Authors. All rights reserved.
   2 #
   3 # SPDX-License-Identifier: CC-BY-SA-3.0
   4
   5 # baseurl is the location of the generated site from the browser's
   6 # perspective (e.g., http://doc.arvados.org or
   7 # file:///tmp/arvados/doc/.site). To make docs show up inside
   8 # workbench, use /doc here and add a symlink at
   9 # apps/workbench/public/doc pointing to ../../../doc/.site
  10 # You can also set these on the command line:
  11 # $ rake generate baseurl=/example arvados_api_host=example.com
  12
  13 baseurl:
  14 current_version:
  15 all_versions:
  16 arvados_api_host: localhost
  17 arvados_cluster_uuid: local
  18 arvados_workbench_host: http://localhost
  19
  20 exclude: ["Rakefile", "tmp", "vendor"]
  21
  22 navbar:
  23   userguide:
  24     - Welcome:
  25       - user/index.html.textile.liquid
  26       - user/getting_started/community.html.textile.liquid
  27     - Walkthough:
  28       - user/tutorials/wgs-tutorial.html.textile.liquid
  29     - Using Workbench:
  30       - user/getting_started/workbench.html.textile.liquid
  31       - user/tutorials/tutorial-workflow-workbench.html.textile.liquid
  32       - user/topics/workbench-migration.html.textile.liquid
  33     - Working at the Command Line:
  34       - user/getting_started/setup-cli.html.textile.liquid
  35       - user/reference/api-tokens.html.textile.liquid
  36       - user/getting_started/check-environment.html.textile.liquid
  37     - Access an Arvados virtual machine:
  38       - user/getting_started/vm-login-with-webshell.html.textile.liquid
  39       - user/getting_started/ssh-access-unix.html.textile.liquid
  40       - user/getting_started/ssh-access-windows.html.textile.liquid
  41     - Working with data sets:
  42       - user/tutorials/tutorial-keep.html.textile.liquid
  43       - user/tutorials/tutorial-keep-get.html.textile.liquid
  44       - user/tutorials/tutorial-keep-mount-gnu-linux.html.textile.liquid
  45       - user/tutorials/tutorial-keep-mount-os-x.html.textile.liquid
  46       - user/tutorials/tutorial-keep-mount-windows.html.textile.liquid
  47       - user/tutorials/tutorial-keep-collection-lifecycle.html.textile.liquid
  48       - user/topics/arv-copy.html.textile.liquid
  49       - user/topics/collection-versioning.html.textile.liquid
  50       - user/topics/storage-classes.html.textile.liquid
  51     - Data Analysis with Workflows:
  52       - user/cwl/arvados-vscode-training.html.md.liquid
  53       - user/cwl/rnaseq-cwl-training.html.textile.liquid
  54       - user/cwl/cwl-runner.html.textile.liquid
  55       - user/cwl/cwl-run-options.html.textile.liquid
  56       - user/tutorials/writing-cwl-workflow.html.textile.liquid
  57       - user/topics/arv-docker.html.textile.liquid
  58       - user/cwl/cwl-style.html.textile.liquid
  59       - user/cwl/cwl-extensions.html.textile.liquid
  60       - user/cwl/federated-workflows.html.textile.liquid
  61       - user/cwl/cwl-versions.html.textile.liquid
  62       - user/cwl/crunchstat-summary.html.textile.liquid
  63       - user/cwl/costanalyzer.html.textile.liquid
  64       - user/debugging/container-shell-access.html.textile.liquid
  65     - Working with git repositories:
  66       - user/tutorials/add-new-repository.html.textile.liquid
  67       - user/tutorials/git-arvados-guide.html.textile.liquid
  68     - Reference:
  69       - user/topics/link-accounts.html.textile.liquid
  70       - user/reference/cookbook.html.textile.liquid
  71     - Arvados License:
  72       - user/copying/copying.html.textile.liquid
  73       - user/copying/agpl-3.0.html
  74       - user/copying/LICENSE-2.0.html
  75       - user/copying/by-sa-3.0.html
  76   sdk:
  77     - Overview:
  78       - sdk/index.html.textile.liquid
  79     - Python:
  80       - sdk/python/sdk-python.html.textile.liquid
  81       - sdk/python/api-client.html.textile.liquid
  82       - sdk/python/cookbook.html.textile.liquid
  83       - sdk/python/python.html.textile.liquid
  84       - sdk/python/arvados-fuse.html.textile.liquid
  85       - sdk/python/arvados-cwl-runner.html.textile.liquid
  86       - sdk/python/events.html.textile.liquid
  87     - CLI:
  88       - sdk/cli/install.html.textile.liquid
  89       - sdk/cli/index.html.textile.liquid
  90       - sdk/cli/reference.html.textile.liquid
  91       - sdk/cli/subcommands.html.textile.liquid
  92       - sdk/cli/project-management.html.textile.liquid
  93     - Go:
  94       - sdk/go/index.html.textile.liquid
  95       - sdk/go/example.html.textile.liquid
  96     - R:
  97       - sdk/R/index.html.md
  98       - sdk/R/arvados/index.html.textile.liquid
  99     - Ruby:
 100       - sdk/ruby/index.html.textile.liquid
 101       - sdk/ruby/example.html.textile.liquid
 102     - Java v2:
 103       - sdk/java-v2/index.html.textile.liquid
 104       - sdk/java-v2/example.html.textile.liquid
 105       - sdk/java-v2/javadoc.html.textile.liquid
 106   api:
 107     - Concepts:
 108       - api/index.html.textile.liquid
 109       - api/tokens.html.textile.liquid
 110       - api/requests.html.textile.liquid
 111       - api/methods.html.textile.liquid
 112       - api/resources.html.textile.liquid
 113     - Permission and authentication:
 114       - api/methods/api_client_authorizations.html.textile.liquid
 115       - api/methods/api_clients.html.textile.liquid
 116       - api/methods/authorized_keys.html.textile.liquid
 117       - api/methods/groups.html.textile.liquid
 118       - api/methods/users.html.textile.liquid
 119       - api/methods/user_agreements.html.textile.liquid
 120     - System resources:
 121       - api/methods/keep_services.html.textile.liquid
 122       - api/methods/links.html.textile.liquid
 123       - api/methods/logs.html.textile.liquid
 124       - api/methods/nodes.html.textile.liquid
 125       - api/methods/virtual_machines.html.textile.liquid
 126       - api/methods/keep_disks.html.textile.liquid
 127     - Data management:
 128       - api/keep-webdav.html.textile.liquid
 129       - api/keep-s3.html.textile.liquid
 130       - api/keep-web-urls.html.textile.liquid
 131       - api/projects.html.textile.liquid
 132       - api/properties.html.textile.liquid
 133       - api/methods/collections.html.textile.liquid
 134       - api/methods/repositories.html.textile.liquid
 135     - Container engine:
 136       - api/methods/container_requests.html.textile.liquid
 137       - api/methods/containers.html.textile.liquid
 138       - api/methods/workflows.html.textile.liquid
 139     - Management (admin/system):
 140       - api/dispatch.html.textile.liquid
 141     - Jobs engine (legacy):
 142       - api/crunch-scripts.html.textile.liquid
 143       - api/methods/jobs.html.textile.liquid
 144       - api/methods/job_tasks.html.textile.liquid
 145       - api/methods/pipeline_instances.html.textile.liquid
 146       - api/methods/pipeline_templates.html.textile.liquid
 147     - Metadata for bioinformatics (deprecated):
 148       - api/methods/humans.html.textile.liquid
 149       - api/methods/specimens.html.textile.liquid
 150       - api/methods/traits.html.textile.liquid
 151   architecture:
 152     - Topics:
 153       - architecture/index.html.textile.liquid
 154     - Storage in Keep:
 155       - architecture/storage.html.textile.liquid
 156       - architecture/keep-components-overview.html.textile.liquid
 157       - architecture/keep-clients.html.textile.liquid
 158       - architecture/keep-data-lifecycle.html.textile.liquid
 159       - architecture/manifest-format.html.textile.liquid
 160     - Computation with Crunch:
 161       - api/execution.html.textile.liquid
 162       - architecture/dispatchcloud.html.textile.liquid
 163       - architecture/hpc.html.textile.liquid
 164       - architecture/singularity.html.textile.liquid
 165     - Other:
 166       - api/permission-model.html.textile.liquid
 167       - architecture/federation.html.textile.liquid
 168   admin:
 169     - Topics:
 170       - admin/index.html.textile.liquid
 171     - Users and Groups:
 172       - admin/user-management.html.textile.liquid
 173       - admin/user-management-cli.html.textile.liquid
 174       - admin/group-management.html.textile.liquid
 175       - admin/reassign-ownership.html.textile.liquid
 176       - admin/link-accounts.html.textile.liquid
 177       - admin/federation.html.textile.liquid
 178       - admin/merge-remote-account.html.textile.liquid
 179       - admin/migrating-providers.html.textile.liquid
 180       - user/topics/arvados-sync-external-sources.html.textile.liquid
 181       - admin/scoped-tokens.html.textile.liquid
 182       - admin/token-expiration-policy.html.textile.liquid
 183     - Monitoring:
 184       - admin/logging.html.textile.liquid
 185       - admin/metrics.html.textile.liquid
 186       - admin/health-checks.html.textile.liquid
 187       - admin/diagnostics.html.textile.liquid
 188       - admin/management-token.html.textile.liquid
 189       - admin/user-activity.html.textile.liquid
 190     - Data Management:
 191       - admin/collection-versioning.html.textile.liquid
 192       - admin/collection-managed-properties.html.textile.liquid
 193       - admin/restricting-upload-download.html.textile.liquid
 194       - admin/keep-balance.html.textile.liquid
 195       - admin/controlling-container-reuse.html.textile.liquid
 196       - admin/logs-table-management.html.textile.liquid
 197       - admin/metadata-vocabulary.html.textile.liquid
 198       - admin/storage-classes.html.textile.liquid
 199       - admin/keep-recovering-data.html.textile.liquid
 200       - admin/keep-measuring-deduplication.html.textile.liquid
 201     - Cloud:
 202       - admin/spot-instances.html.textile.liquid
 203       - admin/cloudtest.html.textile.liquid
 204     - Other:
 205       - install/migrate-docker19.html.textile.liquid
 206       - admin/upgrade-crunch2.html.textile.liquid
 207   installguide:
 208     - Overview:
 209       - install/index.html.textile.liquid
 210     - Docker quick start:
 211       - install/arvbox.html.textile.liquid
 212     - Arvados Installer:
 213       - install/salt-single-host.html.textile.liquid
 214       - install/salt-multi-host.html.textile.liquid
 215 #    - Arvados on Kubernetes:
 216 #      - install/arvados-on-kubernetes.html.textile.liquid
 217 #      - install/arvados-on-kubernetes-minikube.html.textile.liquid
 218 #      - install/arvados-on-kubernetes-GKE.html.textile.liquid
 219     - Manual installation:
 220       - install/install-manual-prerequisites.html.textile.liquid
 221       - install/packages.html.textile.liquid
 222     - Configuration:
 223       - install/config.html.textile.liquid
 224       - admin/config-urls.html.textile.liquid
 225       - admin/config.html.textile.liquid
 226     - Maintenance and upgrading:
 227       - admin/upgrading.html.textile.liquid
 228       - admin/maintenance-and-upgrading.html.textile.liquid
 229     - Core:
 230       - install/install-api-server.html.textile.liquid
 231       - install/diagnostics.html.textile.liquid
 232     - Keep:
 233       - install/install-keepstore.html.textile.liquid
 234       - install/configure-fs-storage.html.textile.liquid
 235       - install/configure-s3-object-storage.html.textile.liquid
 236       - install/configure-azure-blob-storage.html.textile.liquid
 237       - install/install-keepproxy.html.textile.liquid
 238       - install/install-keep-web.html.textile.liquid
 239       - install/install-keep-balance.html.textile.liquid
 240     - User interface:
 241       - install/setup-login.html.textile.liquid
 242       - install/install-ws.html.textile.liquid
 243       - install/install-workbench-app.html.textile.liquid
 244       - install/install-workbench2-app.html.textile.liquid
 245 #      - install/install-composer.html.textile.liquid
 246     - Additional services:
 247       - install/install-shell-server.html.textile.liquid
 248       - install/install-webshell.html.textile.liquid
 249       - install/install-arv-git-httpd.html.textile.liquid
 250 #    - Containers API (all):
 251 #      - install/install-jobs-image.html.textile.liquid
 252     - Containers API (cloud):
 253       - install/crunch2-cloud/install-compute-node.html.textile.liquid
 254       - install/crunch2-cloud/install-dispatch-cloud.html.textile.liquid
 255     - Compute nodes (Slurm or LSF):
 256       - install/crunch2/install-compute-node-docker.html.textile.liquid
 257       - install/crunch2/install-compute-node-singularity.html.textile.liquid
 258     - Containers API (Slurm):
 259       - install/crunch2-slurm/install-dispatch.html.textile.liquid
 260       - install/crunch2-slurm/configure-slurm.html.textile.liquid
 261       - install/crunch2-slurm/install-test.html.textile.liquid
 262     - Containers API (LSF):
 263       - install/crunch2-lsf/install-dispatch.html.textile.liquid
 264     - Additional configuration:
 265       - install/container-shell-access.html.textile.liquid
 266     - External dependencies:
 267       - install/install-postgresql.html.textile.liquid
 268       - install/ruby.html.textile.liquid
 269       - install/nginx.html.textile.liquid
 270       - install/install-docker.html.textile.liquid