# $ 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"]
- 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/tutorials/tutorial-keep-collection-lifecycle.html.textile.liquid
- - user/tutorials/tutorial-keep-mount.html.textile.liquid
- - user/topics/keep.html.textile.liquid
- user/topics/arv-copy.html.textile.liquid
+ - user/topics/collection-versioning.html.textile.liquid
- user/topics/storage-classes.html.textile.liquid
- - Running workflows at the command line:
+ - 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
- - 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/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
+ - 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
- 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
- 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
- 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
- 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/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
- - 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-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
+ - Other:
- api/permission-model.html.textile.liquid
- architecture/federation.html.textile.liquid
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/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:
+ - 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/workbench2-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/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
- 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
- - install/crunch2-slurm/install-compute-node.html.textile.liquid
+ - Containers API (cloud):
+ - 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
+ - Containers API (slurm):
- install/crunch2-slurm/install-dispatch.html.textile.liquid
+ - install/crunch2-slurm/configure-slurm.html.textile.liquid
+ - install/crunch2-slurm/install-compute-node.html.textile.liquid
- install/crunch2-slurm/install-test.html.textile.liquid
- - install/install-nodemanager.html.textile.liquid
- - install/install-compute-ping.html.textile.liquid
- - Jobs API support (deprecated):
- - install/install-crunch-dispatch.html.textile.liquid
- - install/install-compute-node.html.textile.liquid
+ - Containers API (lsf):
+ - install/crunch2-lsf/install-dispatch.html.textile.liquid
+ - Additional configuration:
+ - install/singularity.html.textile.liquid
+ - 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