- user/tutorials/tutorial-keep-mount.html.textile.liquid
- user/topics/keep.html.textile.liquid
- user/topics/arv-copy.html.textile.liquid
- - Run a pipeline on the command line:
+ - 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 Arvados Repositories:
+ - Working with git repositories:
- user/tutorials/add-new-repository.html.textile.liquid
- - Develop a new pipeline:
+ - user/tutorials/git-arvados-guide.html.textile.liquid
+ - Develop an Arvados pipeline:
- user/tutorials/intro-crunch.html.textile.liquid
- user/tutorials/running-external-program.html.textile.liquid
- user/topics/crunch-tools-overview.html.textile.liquid
api:
- Concepts:
- api/index.html.textile.liquid
- - api/authentication.html.textile.liquid
+ - api/requests.html.textile.liquid
- api/methods.html.textile.liquid
- api/resources.html.textile.liquid
- - api/crunch-scripts.html.textile.liquid
- api/permission-model.html.textile.liquid
- - API Methods:
+ - Permission and authentication:
+ - api/methods/users.html.textile.liquid
+ - api/methods/groups.html.textile.liquid
- api/methods/api_client_authorizations.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/groups.html.textile.liquid
- - api/methods/humans.html.textile.liquid
- - api/methods/jobs.html.textile.liquid
- - api/methods/job_tasks.html.textile.liquid
- - api/methods/keep_disks.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
- - api/methods/repositories.html.textile.liquid
+ - Metadata for bioinformatics:
+ - api/methods/humans.html.textile.liquid
- api/methods/specimens.html.textile.liquid
- api/methods/traits.html.textile.liquid
- - api/methods/users.html.textile.liquid
- - api/methods/virtual_machines.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/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
- - api/schema/PipelineInstance.html.textile.liquid
- - api/schema/PipelineTemplate.html.textile.liquid
- - api/schema/Repository.html.textile.liquid
- - api/schema/Specimen.html.textile.liquid
- - api/schema/Trait.html.textile.liquid
- - api/schema/User.html.textile.liquid
- - api/schema/VirtualMachine.html.textile.liquid
installguide:
- Overview:
- install/index.html.textile.liquid
- - Docker-based installation:
- - install/pre-built-docker.html.textile.liquid
- - install/install-docker.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-arv-git-httpd.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