# 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:
+baseurl:
arvados_api_host: localhost
arvados_workbench_host: localhost
userguide:
- Getting Started:
- 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/getting_started/ssh-access.html.textile.liquid
+ - user/tutorials/tutorial-pipeline-workbench.html.textile.liquid
+ - Access an Arvados virtual machine:
+ - 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
+ - Run a pipeline on the command line:
+ - user/topics/running-pipeline-command-line.html.textile.liquid
+ - user/topics/arv-run.html.textile.liquid
+ - user/reference/sdk-cli.html.textile.liquid
+ - Develop a new 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/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/topics/run-command.html.textile.liquid
- user/examples/crunch-examples.html.textile.liquid
- - Reference:
- - user/reference/api-tokens.html.textile.liquid
- - user/reference/sdk-cli.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
- sdk/python/sdk-python.html.textile.liquid
- sdk/python/python.html.textile.liquid
- sdk/python/crunch-utility-libraries.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
api:
- Concepts:
- api/index.html.textile.liquid
- api/methods/jobs.html.textile.liquid
- api/methods/job_tasks.html.textile.liquid
- api/methods/keep_disks.html.textile.liquid
+ - 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/schema/ApiClient.html.textile.liquid
- api/schema/AuthorizedKey.html.textile.liquid
- api/schema/Collection.html.textile.liquid
- - api/schema/CommitAncestor.html.textile.liquid
- - api/schema/Commit.html.textile.liquid
- api/schema/Group.html.textile.liquid
- api/schema/Human.html.textile.liquid
- api/schema/Job.html.textile.liquid
- api/schema/JobTask.html.textile.liquid
- api/schema/KeepDisk.html.textile.liquid
+ - api/schema/KeepService.html.textile.liquid
- api/schema/Link.html.textile.liquid
- api/schema/Log.html.textile.liquid
- api/schema/Node.html.textile.liquid
- admin/index.html.md.liquid
- admin/cheat_sheet.html.textile.liquid
installguide:
- - Install:
- - install/index.html.md.liquid
- - install/install-api-server.html.md.liquid
- - install/install-workbench-app.html.md.liquid
- - install/client.html.textile.liquid
+ - Overview:
+ - install/index.html.textile.liquid
+ - Docker:
+ - install/install-docker.html.textile.liquid
+ - Manual installation:
+ - install/install-keep.html.textile.liquid
+ - install/install-sso.html.textile.liquid
+ - install/install-api-server.html.textile.liquid
+ - install/install-workbench-app.html.textile.liquid
- install/create-standard-objects.html.textile.liquid
- install/install-crunch-dispatch.html.textile.liquid