- user/getting_started/community.html.textile.liquid
- Walkthough:
- user/tutorials/wgs-tutorial.html.textile.liquid
- - Run a workflow using Workbench:
+ - Using Workbench:
- user/getting_started/workbench.html.textile.liquid
- user/tutorials/tutorial-workflow-workbench.html.textile.liquid
+ - user/topics/workbench-migration.html.textile.liquid
- Working at the Command Line:
- user/getting_started/setup-cli.html.textile.liquid
- user/reference/api-tokens.html.textile.liquid
- user/topics/storage-classes.html.textile.liquid
- Data Analysis with Workflows:
- user/cwl/arvados-vscode-training.html.md.liquid
+ - user/cwl/rnaseq-cwl-training.html.textile.liquid
- user/cwl/cwl-runner.html.textile.liquid
- user/cwl/cwl-run-options.html.textile.liquid
- user/tutorials/writing-cwl-workflow.html.textile.liquid
- sdk/java-v2/index.html.textile.liquid
- sdk/java-v2/example.html.textile.liquid
- sdk/java-v2/javadoc.html.textile.liquid
- - Java v1:
- - sdk/java/index.html.textile.liquid
- - sdk/java/example.html.textile.liquid
- Perl:
- sdk/perl/index.html.textile.liquid
- sdk/perl/example.html.textile.liquid
- Computation with Crunch:
- api/execution.html.textile.liquid
- architecture/dispatchcloud.html.textile.liquid
+ - architecture/singularity.html.textile.liquid
- Other:
- api/permission-model.html.textile.liquid
- architecture/federation.html.textile.liquid
- admin/keep-balance.html.textile.liquid
- admin/controlling-container-reuse.html.textile.liquid
- admin/logs-table-management.html.textile.liquid
- - admin/workbench2-vocabulary.html.textile.liquid
+ - admin/metadata-vocabulary.html.textile.liquid
- admin/storage-classes.html.textile.liquid
- admin/keep-recovering-data.html.textile.liquid
- admin/keep-measuring-deduplication.html.textile.liquid
- Manual installation:
- install/install-manual-prerequisites.html.textile.liquid
- install/packages.html.textile.liquid
- - admin/upgrading.html.textile.liquid
- Configuration:
- install/config.html.textile.liquid
- - admin/config-migration.html.textile.liquid
+ - admin/config-urls.html.textile.liquid
- admin/config.html.textile.liquid
+ - Maintenance and upgrading:
+ - admin/upgrading.html.textile.liquid
+ - admin/maintenance-and-upgrading.html.textile.liquid
- Core:
- install/install-api-server.html.textile.liquid
- Keep:
- install/install-shell-server.html.textile.liquid
- install/install-webshell.html.textile.liquid
- install/install-arv-git-httpd.html.textile.liquid
- - Containers API (cloud):
+ - Containers API (all):
- install/install-jobs-image.html.textile.liquid
+ - Containers API (cloud):
- install/crunch2-cloud/install-compute-node.html.textile.liquid
- install/crunch2-cloud/install-dispatch-cloud.html.textile.liquid
- - Containers API (slurm):
+ - Compute nodes (Slurm or LSF):
+ - install/crunch2/install-compute-node-docker.html.textile.liquid
+ - install/crunch2/install-compute-node-singularity.html.textile.liquid
+ - Containers API (Slurm):
- install/crunch2-slurm/install-dispatch.html.textile.liquid
- install/crunch2-slurm/configure-slurm.html.textile.liquid
- - install/crunch2-slurm/install-compute-node.html.textile.liquid
- install/crunch2-slurm/install-test.html.textile.liquid
- - Containers API (lsf):
+ - Containers API (LSF):
- install/crunch2-lsf/install-dispatch.html.textile.liquid
- Additional configuration:
- - install/singularity.html.textile.liquid
- install/container-shell-access.html.textile.liquid
- External dependencies:
- install/install-postgresql.html.textile.liquid