# Copyright (C) The Arvados Authors. All rights reserved. # # SPDX-License-Identifier: CC-BY-SA-3.0 # baseurl is the location of the generated site from the browser's # perspective (e.g., http://doc.arvados.org or # file:///tmp/arvados/doc/.site). To make docs show up inside # workbench, use /doc here and add a symlink at # apps/workbench/public/doc pointing to ../../../doc/.site # You can also set these on the command line: # $ 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 exclude: ["Rakefile", "tmp", "vendor"] navbar: userguide: - 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 - 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 - 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/tutorials/tutorial-keep-collection-lifecycle.html.textile.liquid - user/topics/arv-copy.html.textile.liquid - user/topics/collection-versioning.html.textile.liquid - user/topics/storage-classes.html.textile.liquid - Data Analysis with Workflows: - user/cwl/arvados-vscode-training.html.md.liquid - user/cwl/cwl-runner.html.textile.liquid - user/cwl/cwl-run-options.html.textile.liquid - user/tutorials/writing-cwl-workflow.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/cwl/federated-workflows.html.textile.liquid - user/cwl/cwl-versions.html.textile.liquid - user/cwl/crunchstat-summary.html.textile.liquid - user/cwl/costanalyzer.html.textile.liquid - user/debugging/container-shell-access.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 - Arvados License: - user/copying/copying.html.textile.liquid - user/copying/agpl-3.0.html - user/copying/LICENSE-2.0.html - user/copying/by-sa-3.0.html sdk: - Overview: - sdk/index.html.textile.liquid - Python: - sdk/python/sdk-python.html.textile.liquid - sdk/python/example.html.textile.liquid - sdk/python/python.html.textile.liquid - sdk/python/arvados-fuse.html.textile.liquid - sdk/python/arvados-cwl-runner.html.textile.liquid - sdk/python/cookbook.html.textile.liquid - sdk/python/events.html.textile.liquid - CLI: - sdk/cli/install.html.textile.liquid - sdk/cli/index.html.textile.liquid - sdk/cli/reference.html.textile.liquid - sdk/cli/subcommands.html.textile.liquid - Go: - sdk/go/index.html.textile.liquid - sdk/go/example.html.textile.liquid - R: - sdk/R/index.html.md - sdk/R/arvados/index.html.textile.liquid - Ruby: - sdk/ruby/index.html.textile.liquid - sdk/ruby/example.html.textile.liquid - 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 - api/tokens.html.textile.liquid - api/requests.html.textile.liquid - api/methods.html.textile.liquid - api/resources.html.textile.liquid - Permission and authentication: - api/methods/api_client_authorizations.html.textile.liquid - api/methods/api_clients.html.textile.liquid - 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 - api/methods/logs.html.textile.liquid - api/methods/nodes.html.textile.liquid - 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/projects.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 - 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 (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 - Storage in Keep: - architecture/storage.html.textile.liquid - architecture/keep-components-overview.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 - architecture/dispatchcloud.html.textile.liquid - architecture/singularity.html.textile.liquid - Other: - api/permission-model.html.textile.liquid - architecture/federation.html.textile.liquid admin: - Topics: - admin/index.html.textile.liquid - Users and Groups: - 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/logging.html.textile.liquid - admin/metrics.html.textile.liquid - admin/health-checks.html.textile.liquid - admin/management-token.html.textile.liquid - Data Management: - admin/collection-versioning.html.textile.liquid - admin/collection-managed-properties.html.textile.liquid - admin/restricting-upload-download.html.textile.liquid - admin/keep-balance.html.textile.liquid - admin/controlling-container-reuse.html.textile.liquid - admin/logs-table-management.html.textile.liquid - admin/metadata-vocabulary.html.textile.liquid - admin/storage-classes.html.textile.liquid - admin/keep-recovering-data.html.textile.liquid - admin/keep-measuring-deduplication.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 - Manual installation: - install/install-manual-prerequisites.html.textile.liquid - install/packages.html.textile.liquid - Configuration: - install/config.html.textile.liquid - admin/config-urls.html.textile.liquid - admin/config.html.textile.liquid - Maintenance and upgrading: - admin/upgrading.html.textile.liquid - admin/maintenance-and-upgrading.html.textile.liquid - Core: - install/install-api-server.html.textile.liquid - Keep: - install/install-keepstore.html.textile.liquid - install/configure-fs-storage.html.textile.liquid - install/configure-s3-object-storage.html.textile.liquid - install/configure-azure-blob-storage.html.textile.liquid - install/install-keepproxy.html.textile.liquid - install/install-keep-web.html.textile.liquid - install/install-keep-balance.html.textile.liquid - User interface: - 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-shell-server.html.textile.liquid - install/install-webshell.html.textile.liquid - install/install-arv-git-httpd.html.textile.liquid - Containers API (all): - install/install-jobs-image.html.textile.liquid - Containers API (cloud): - install/crunch2-cloud/install-compute-node.html.textile.liquid - install/crunch2-cloud/install-dispatch-cloud.html.textile.liquid - Compute nodes (Slurm or LSF): - install/crunch2/install-compute-node-docker.html.textile.liquid - install/crunch2/install-compute-node-singularity.html.textile.liquid - Containers API (Slurm): - install/crunch2-slurm/install-dispatch.html.textile.liquid - install/crunch2-slurm/configure-slurm.html.textile.liquid - install/crunch2-slurm/install-test.html.textile.liquid - Containers API (LSF): - install/crunch2-lsf/install-dispatch.html.textile.liquid - Additional configuration: - install/container-shell-access.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