# 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
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
+ - 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/examples/crunch-examples.html.textile.liquid
+ - user/topics/arv-docker.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/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
- Docker:
- install/install-docker.html.textile.liquid
- Manual installation:
- - install/install-sso.html.textile.liquid
+ - install/install-manual-overview.html.textile.liquid
+ - install/install-manual-prerequisites.html.textile.liquid
- install/install-api-server.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/install-keepproxy.html.textile.liquid
- install/install-crunch-dispatch.html.textile.liquid
+ - install/install-compute-node.html.textile.liquid
+ - Software prerequisites:
+ - install/install-manual-prerequisites-ruby.html.textile.liquid
+ - install/install-sso.html.textile.liquid