# 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: arvados_api_host: localhost arvados_workbench_host: http://localhost exclude: ["Rakefile", "tmp", "vendor"] navbar: #start: #- Getting Started: #- start/index.html.textile.liquid #- Quickstart: #- start/getting_started/publicproject.html.textile.liquid #- start/getting_started/firstpipeline.html.textile.liquid #- Common Use Cases: #- start/getting_started/sharedata.html.textile.liquid #- Next Steps: #- start/getting_started/nextsteps.html.textile.liquid userguide: - Welcome: - user/index.html.textile.liquid - user/getting_started/community.html.textile.liquid - Run a workflow using Workbench: - user/getting_started/workbench.html.textile.liquid - user/tutorials/tutorial-workflow-workbench.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-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 - Running workflows at the command line: - user/cwl/cwl-runner.html.textile.liquid - user/cwl/cwl-run-options.html.textile.liquid - user/topics/running-pipeline-command-line.html.textile.liquid - user/topics/arv-run.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/cwl-style.html.textile.liquid - user/cwl/cwl-extensions.html.textile.liquid - user/topics/arv-docker.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 - Develop a web service: - user/topics/arv-web.html.textile.liquid - Reference: - user/topics/run-command.html.textile.liquid - user/reference/job-pipeline-ref.html.textile.liquid - user/examples/crunch-examples.html.textile.liquid - Query the metadata database: - user/topics/tutorial-trait-search.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/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 - 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 - 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: - sdk/java/index.html.textile.liquid - sdk/java/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 - api/permission-model.html.textile.liquid - api/storage.html.textile.liquid - api/execution.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 - 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/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): - 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: - api/methods/humans.html.textile.liquid - api/methods/specimens.html.textile.liquid - api/methods/traits.html.textile.liquid installguide: - Overview: - install/index.html.textile.liquid - Docker quick start: - install/arvbox.html.textile.liquid - Manual installation: - install/install-manual-prerequisites.html.textile.liquid - install/install-postgresql.html.textile.liquid - install/install-sso.html.textile.liquid - install/install-api-server.html.textile.liquid - install/install-ws.html.textile.liquid - install/install-arv-git-httpd.html.textile.liquid - install/install-workbench-app.html.textile.liquid - install/install-shell-server.html.textile.liquid - install/create-standard-objects.html.textile.liquid - install/install-keepstore.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 - 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 - 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 - Jobs API support (deprecated): - install/install-crunch-dispatch.html.textile.liquid - install/install-compute-node.html.textile.liquid - Helpful hints: - install/copy_pipeline_from_curoverse.html.textile.liquid - install/cheat_sheet.html.textile.liquid - Migrating from Docker 1.9: - install/migrate-docker19.html.textile.liquid