# 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.comA
+# $ rake generate baseurl=/example arvados_api_host=example.com
baseurl:
arvados_api_host: localhost
-arvados_workbench_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:
- - Getting Started:
+ - Welcome:
- user/index.html.textile.liquid
+ - user/getting_started/community.html.textile.liquid
+ - Run a pipeline using Workbench:
- user/getting_started/workbench.html.textile.liquid
+ - user/tutorials/tutorial-pipeline-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/getting_started/community.html.textile.liquid
- - Tutorials:
+ - 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.html.textile.liquid
+ - user/topics/keep.html.textile.liquid
+ - user/topics/arv-copy.html.textile.liquid
+ - Using Common Workflow Language:
+ - user/cwl/cwl-runner.html.textile.liquid
+ - user/cwl/cwl-style.html.textile.liquid
+ - Working on the command line:
+ - 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 pipeline:
- user/tutorials/intro-crunch.html.textile.liquid
- - user/tutorials/tutorial-pipeline-workbench.html.textile.liquid
- - user/tutorials/tutorial-firstscript.html.textile.liquid
- - user/tutorials/tutorial-new-pipeline.html.textile.liquid
- user/tutorials/running-external-program.html.textile.liquid
- - Intermediate topics:
- - user/topics/running-pipeline-command-line.html.textile.liquid
- - user/topics/tutorial-job1.html.textile.liquid
- - user/topics/tutorial-job-debug.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/tutorial-trait-search.html.textile.liquid
- - user/topics/tutorial-gatk-variantfiltration.html.textile.liquid
- - user/topics/keep.html.textile.liquid
- - Examples:
- - user/examples/crunch-examples.html.textile.liquid
+ - user/topics/arv-docker.html.textile.liquid
+ - Develop a web service:
+ - user/topics/arv-web.html.textile.liquid
- Reference:
- - user/reference/api-tokens.html.textile.liquid
- - user/reference/sdk-cli.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
+ - 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
- sdk/python/sdk-python.html.textile.liquid
- sdk/python/python.html.textile.liquid
- sdk/python/crunch-utility-libraries.html.textile.liquid
+ - sdk/python/events.html.textile.liquid
- Perl:
- sdk/perl/index.html.textile.liquid
- Ruby:
- sdk/ruby/index.html.textile.liquid
- Java:
- sdk/java/index.html.textile.liquid
+ - Go:
+ - sdk/go/index.html.textile.liquid
- CLI:
- sdk/cli/index.html.textile.liquid
+ - sdk/cli/install.html.textile.liquid
+ - sdk/cli/reference.html.textile.liquid
+ - sdk/cli/subcommands.html.textile.liquid
api:
- Concepts:
- api/index.html.textile.liquid
- api/methods/api_clients.html.textile.liquid
- api/methods/authorized_keys.html.textile.liquid
- api/methods/collections.html.textile.liquid
+ - api/methods/container_requests.html.textile.liquid
+ - api/methods/containers.html.textile.liquid
- api/methods/groups.html.textile.liquid
- api/methods/humans.html.textile.liquid
- api/methods/jobs.html.textile.liquid
- api/methods/traits.html.textile.liquid
- api/methods/users.html.textile.liquid
- api/methods/virtual_machines.html.textile.liquid
+ - api/methods/workflows.html.textile.liquid
- Schema:
- api/schema/ApiClientAuthorization.html.textile.liquid
- api/schema/ApiClient.html.textile.liquid
- api/schema/AuthorizedKey.html.textile.liquid
- api/schema/Collection.html.textile.liquid
+ - api/schema/Container.html.textile.liquid
+ - api/schema/ContainerRequest.html.textile.liquid
- api/schema/Group.html.textile.liquid
- api/schema/Human.html.textile.liquid
- api/schema/Job.html.textile.liquid
- api/schema/Trait.html.textile.liquid
- api/schema/User.html.textile.liquid
- api/schema/VirtualMachine.html.textile.liquid
- admin:
- - Admin:
- - admin/index.html.md.liquid
- - admin/cheat_sheet.html.textile.liquid
+ - api/schema/Workflow.html.textile.liquid
installguide:
- Overview:
- install/index.html.textile.liquid
- - Docker:
- - install/install-docker.html.textile.liquid
+ - Docker quick start:
+ - install/arvbox.html.textile.liquid
- Manual installation:
- - install/install-keep.html.textile.liquid
+ - 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-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 Crunch v2 on SLURM:
+ - install/crunch2-slurm/install-prerequisites.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 Crunch v1:
- 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
projects / arvados.git / blobdiff