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Merge branch '19466-cwl-io' refs #19466
[arvados.git]
/
doc
/
_config.yml
diff --git
a/doc/_config.yml
b/doc/_config.yml
index ff924e2f378381f4c8f4e586f3c2c3570d8202e2..aac4256b175d7d6e2d94f28f9a4b9baf4834917d 100644
(file)
--- a/
doc/_config.yml
+++ b/
doc/_config.yml
@@
-26,9
+26,10
@@
navbar:
- user/getting_started/community.html.textile.liquid
- Walkthough:
- user/tutorials/wgs-tutorial.html.textile.liquid
- user/getting_started/community.html.textile.liquid
- Walkthough:
- user/tutorials/wgs-tutorial.html.textile.liquid
- -
Run a workflow u
sing Workbench:
+ -
U
sing Workbench:
- user/getting_started/workbench.html.textile.liquid
- user/tutorials/tutorial-workflow-workbench.html.textile.liquid
- 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
- Working at the Command Line:
- user/getting_started/setup-cli.html.textile.liquid
- user/reference/api-tokens.html.textile.liquid
@@
-49,6
+50,7
@@
navbar:
- user/topics/storage-classes.html.textile.liquid
- Data Analysis with Workflows:
- user/cwl/arvados-vscode-training.html.md.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
- user/cwl/cwl-runner.html.textile.liquid
- user/cwl/cwl-run-options.html.textile.liquid
- user/tutorials/writing-cwl-workflow.html.textile.liquid
@@
-87,6
+89,7
@@
navbar:
- sdk/cli/index.html.textile.liquid
- sdk/cli/reference.html.textile.liquid
- sdk/cli/subcommands.html.textile.liquid
- sdk/cli/index.html.textile.liquid
- sdk/cli/reference.html.textile.liquid
- sdk/cli/subcommands.html.textile.liquid
+ - sdk/cli/project-management.html.textile.liquid
- Go:
- sdk/go/index.html.textile.liquid
- sdk/go/example.html.textile.liquid
- Go:
- sdk/go/index.html.textile.liquid
- sdk/go/example.html.textile.liquid
@@
-100,9
+103,6
@@
navbar:
- sdk/java-v2/index.html.textile.liquid
- sdk/java-v2/example.html.textile.liquid
- sdk/java-v2/javadoc.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
- Perl:
- sdk/perl/index.html.textile.liquid
- sdk/perl/example.html.textile.liquid
@@
-132,6
+132,7
@@
navbar:
- api/keep-s3.html.textile.liquid
- api/keep-web-urls.html.textile.liquid
- api/projects.html.textile.liquid
- api/keep-s3.html.textile.liquid
- api/keep-web-urls.html.textile.liquid
- api/projects.html.textile.liquid
+ - api/properties.html.textile.liquid
- api/methods/collections.html.textile.liquid
- api/methods/repositories.html.textile.liquid
- Container engine:
- api/methods/collections.html.textile.liquid
- api/methods/repositories.html.textile.liquid
- Container engine:
@@
-162,6
+163,8
@@
navbar:
- Computation with Crunch:
- api/execution.html.textile.liquid
- architecture/dispatchcloud.html.textile.liquid
- Computation with Crunch:
- api/execution.html.textile.liquid
- architecture/dispatchcloud.html.textile.liquid
+ - architecture/hpc.html.textile.liquid
+ - architecture/singularity.html.textile.liquid
- Other:
- api/permission-model.html.textile.liquid
- architecture/federation.html.textile.liquid
- Other:
- api/permission-model.html.textile.liquid
- architecture/federation.html.textile.liquid
@@
-171,21
+174,21
@@
navbar:
- Users and Groups:
- admin/user-management.html.textile.liquid
- admin/user-management-cli.html.textile.liquid
- Users and Groups:
- admin/user-management.html.textile.liquid
- admin/user-management-cli.html.textile.liquid
+ - admin/group-management.html.textile.liquid
- admin/reassign-ownership.html.textile.liquid
- admin/link-accounts.html.textile.liquid
- admin/reassign-ownership.html.textile.liquid
- admin/link-accounts.html.textile.liquid
- - admin/group-management.html.textile.liquid
- admin/federation.html.textile.liquid
- admin/merge-remote-account.html.textile.liquid
- admin/migrating-providers.html.textile.liquid
- admin/federation.html.textile.liquid
- admin/merge-remote-account.html.textile.liquid
- admin/migrating-providers.html.textile.liquid
- - user/topics/arvados-sync-
group
s.html.textile.liquid
+ - user/topics/arvados-sync-
external-source
s.html.textile.liquid
- admin/scoped-tokens.html.textile.liquid
- admin/token-expiration-policy.html.textile.liquid
- admin/scoped-tokens.html.textile.liquid
- admin/token-expiration-policy.html.textile.liquid
- - admin/user-activity.html.textile.liquid
- Monitoring:
- admin/logging.html.textile.liquid
- admin/metrics.html.textile.liquid
- admin/health-checks.html.textile.liquid
- admin/management-token.html.textile.liquid
- Monitoring:
- admin/logging.html.textile.liquid
- admin/metrics.html.textile.liquid
- admin/health-checks.html.textile.liquid
- admin/management-token.html.textile.liquid
+ - admin/user-activity.html.textile.liquid
- Data Management:
- admin/collection-versioning.html.textile.liquid
- admin/collection-managed-properties.html.textile.liquid
- Data Management:
- admin/collection-versioning.html.textile.liquid
- admin/collection-managed-properties.html.textile.liquid
@@
-193,7
+196,7
@@
navbar:
- admin/keep-balance.html.textile.liquid
- admin/controlling-container-reuse.html.textile.liquid
- admin/logs-table-management.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
- admin/storage-classes.html.textile.liquid
- admin/keep-recovering-data.html.textile.liquid
- admin/keep-measuring-deduplication.html.textile.liquid
@@
-209,8
+212,6
@@
navbar:
- Docker quick start:
- install/arvbox.html.textile.liquid
- Installation with Salt:
- Docker quick start:
- install/arvbox.html.textile.liquid
- Installation with Salt:
- - install/salt.html.textile.liquid
- - install/salt-vagrant.html.textile.liquid
- install/salt-single-host.html.textile.liquid
- install/salt-multi-host.html.textile.liquid
- Arvados on Kubernetes:
- install/salt-single-host.html.textile.liquid
- install/salt-multi-host.html.textile.liquid
- Arvados on Kubernetes:
@@
-220,11
+221,13
@@
navbar:
- Manual installation:
- install/install-manual-prerequisites.html.textile.liquid
- install/packages.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
- Configuration:
- install/config.html.textile.liquid
- - admin/config-
migration
.html.textile.liquid
+ - admin/config-
urls
.html.textile.liquid
- admin/config.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:
- Core:
- install/install-api-server.html.textile.liquid
- Keep:
@@
-245,19
+248,21
@@
navbar:
- install/install-shell-server.html.textile.liquid
- install/install-webshell.html.textile.liquid
- install/install-arv-git-httpd.html.textile.liquid
- 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
- 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
- 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-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
- 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/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
- install/container-shell-access.html.textile.liquid
- External dependencies:
- install/install-postgresql.html.textile.liquid