[ARVADOS] created: 91e4be41d77d023a06d53879b974ecf5d3b82d94
git at public.curoverse.com
git at public.curoverse.com
Mon Jan 13 09:56:02 EST 2014
at 91e4be41d77d023a06d53879b974ecf5d3b82d94 (commit)
commit 91e4be41d77d023a06d53879b974ecf5d3b82d94
Author: Peter Amstutz <peter.amstutz at curoverse.com>
Date: Mon Jan 13 09:56:33 2014 -0500
Zenweb work in progress
diff --git a/doc/Rakefile b/doc/Rakefile
old mode 100755
new mode 100644
diff --git a/doc/admin/cheat_sheet.textile b/doc/admin/cheat_sheet.textile
index 4c26877..32015f2 100644
--- a/doc/admin/cheat_sheet.textile
+++ b/doc/admin/cheat_sheet.textile
@@ -3,7 +3,7 @@ layout: default
navsection: adminguide
title: Cheat Sheet
navorder: 1
----
+...
h1. Cheat Sheet
diff --git a/doc/admin/index.md b/doc/admin/index.md
index 5c75412..53e4e42 100644
--- a/doc/admin/index.md
+++ b/doc/admin/index.md
@@ -3,7 +3,7 @@ layout: default
navsection: adminguide
title: Overview
navorder: 0
----
+...
{% include alert-stub.html %}
diff --git a/doc/api/authentication.textile b/doc/api/authentication.textile
index d02f834..20dfcf7 100644
--- a/doc/api/authentication.textile
+++ b/doc/api/authentication.textile
@@ -4,7 +4,7 @@ navsection: api
navmenu: Concepts
title: Authentication
navorder: 2
----
+...
h1. Authentication
@@ -37,4 +37,4 @@ A client obtains an access code by means of a standard Oauth 2.0 flow. The acces
h3. Refresh the access code (optional)
-Access codes have a limited lifetime. A refresh token allows an application to request a new access token.
\ No newline at end of file
+Access codes have a limited lifetime. A refresh token allows an application to request a new access token.
diff --git a/doc/api/crunch-scripts.textile b/doc/api/crunch-scripts.textile
index 076a589..dcf004e 100644
--- a/doc/api/crunch-scripts.textile
+++ b/doc/api/crunch-scripts.textile
@@ -4,7 +4,7 @@ navsection: api
navmenu: Concepts
title: Crunch scripts
navorder: 5
----
+...
h2. Crunch scripts
diff --git a/doc/api/index.textile b/doc/api/index.textile
index 11cf0ed..64fe57b 100644
--- a/doc/api/index.textile
+++ b/doc/api/index.textile
@@ -3,7 +3,7 @@ layout: default
navsection: api
title: API Reference
navorder: 0
----
+...
h1. API Reference
diff --git a/doc/api/methods.textile b/doc/api/methods.textile
index fd11ddb..c7ddbc3 100644
--- a/doc/api/methods.textile
+++ b/doc/api/methods.textile
@@ -4,7 +4,7 @@ navsection: api
navmenu: Concepts
title: REST methods
navorder: 3
----
+...
h1. REST Methods
diff --git a/doc/api/methods/api_client_authorizations.textile b/doc/api/methods/api_client_authorizations.textile
index 9564b4d..c9f6d82 100644
--- a/doc/api/methods/api_client_authorizations.textile
+++ b/doc/api/methods/api_client_authorizations.textile
@@ -4,7 +4,7 @@ navsection: api
navmenu: API Methods
title: "api_client_authorizations"
navorder: 1
----
+...
h1. api_client_authorizations
diff --git a/doc/api/methods/api_clients.textile b/doc/api/methods/api_clients.textile
index 9ca50f6..2b014ad 100644
--- a/doc/api/methods/api_clients.textile
+++ b/doc/api/methods/api_clients.textile
@@ -4,7 +4,7 @@ navsection: api
navmenu: API Methods
title: "api_clients"
navorder: 2
----
+...
h1. api_clients
diff --git a/doc/api/methods/authorized_keys.textile b/doc/api/methods/authorized_keys.textile
index 9107a69..e1c5892 100644
--- a/doc/api/methods/authorized_keys.textile
+++ b/doc/api/methods/authorized_keys.textile
@@ -4,7 +4,7 @@ navsection: api
navmenu: API Methods
title: "authorized_keys"
navorder: 3
----
+...
h1. authorized_keys
diff --git a/doc/api/methods/collections.textile b/doc/api/methods/collections.textile
index 49bc7e6..100f86e 100644
--- a/doc/api/methods/collections.textile
+++ b/doc/api/methods/collections.textile
@@ -4,7 +4,7 @@ navsection: api
navmenu: API Methods
title: "collections"
navorder: 4
----
+...
h1. collections
diff --git a/doc/api/methods/groups.textile b/doc/api/methods/groups.textile
index 8484834..8db062d 100644
--- a/doc/api/methods/groups.textile
+++ b/doc/api/methods/groups.textile
@@ -4,7 +4,7 @@ navsection: api
navmenu: API Methods
title: "groups"
navorder: 5
----
+...
h1. groups
diff --git a/doc/api/methods/humans.textile b/doc/api/methods/humans.textile
index 222008a..d395b14 100644
--- a/doc/api/methods/humans.textile
+++ b/doc/api/methods/humans.textile
@@ -4,7 +4,7 @@ navsection: api
navmenu: API Methods
title: "humans"
navorder: 6
----
+...
h1. humans
diff --git a/doc/api/methods/job_tasks.textile b/doc/api/methods/job_tasks.textile
index e6695e6..220cf26 100644
--- a/doc/api/methods/job_tasks.textile
+++ b/doc/api/methods/job_tasks.textile
@@ -4,7 +4,7 @@ navsection: api
navmenu: API Methods
title: "job_tasks"
navorder: 7
----
+...
h1. job_tasks
diff --git a/doc/api/methods/jobs.textile b/doc/api/methods/jobs.textile
index 6d34952..8109387 100644
--- a/doc/api/methods/jobs.textile
+++ b/doc/api/methods/jobs.textile
@@ -4,7 +4,7 @@ navsection: api
navmenu: API Methods
title: "jobs"
navorder: 8
----
+...
h1. jobs
diff --git a/doc/api/methods/keep_disks.textile b/doc/api/methods/keep_disks.textile
index 6239cf8..94eb420 100644
--- a/doc/api/methods/keep_disks.textile
+++ b/doc/api/methods/keep_disks.textile
@@ -4,7 +4,7 @@ navsection: api
navmenu: API Methods
title: "keep_disks"
navorder: 9
----
+...
h1. keep_disks
diff --git a/doc/api/methods/links.textile b/doc/api/methods/links.textile
index 1530956..f046783 100644
--- a/doc/api/methods/links.textile
+++ b/doc/api/methods/links.textile
@@ -4,7 +4,7 @@ navsection: api
navmenu: API Methods
title: "links"
navorder: 10
----
+...
h1. links
diff --git a/doc/api/methods/logs.textile b/doc/api/methods/logs.textile
index 4d8c2f4..600cc3a 100644
--- a/doc/api/methods/logs.textile
+++ b/doc/api/methods/logs.textile
@@ -4,7 +4,7 @@ navsection: api
navmenu: API Methods
title: "logs"
navorder: 11
----
+...
h1. logs
diff --git a/doc/api/methods/nodes.textile b/doc/api/methods/nodes.textile
index 656c085..9521d3f 100644
--- a/doc/api/methods/nodes.textile
+++ b/doc/api/methods/nodes.textile
@@ -4,7 +4,7 @@ navsection: api
navmenu: API Methods
title: "nodes"
navorder: 12
----
+...
h1. nodes
diff --git a/doc/api/methods/pipeline_instances.textile b/doc/api/methods/pipeline_instances.textile
index 32ebe84..f50fe85 100644
--- a/doc/api/methods/pipeline_instances.textile
+++ b/doc/api/methods/pipeline_instances.textile
@@ -4,7 +4,7 @@ navsection: api
navmenu: API Methods
title: "pipeline_instances"
navorder: 13
----
+...
h1. pipeline_instances
diff --git a/doc/api/methods/pipeline_templates.textile b/doc/api/methods/pipeline_templates.textile
index d6f5ce8..fafd240 100644
--- a/doc/api/methods/pipeline_templates.textile
+++ b/doc/api/methods/pipeline_templates.textile
@@ -4,7 +4,7 @@ navsection: api
navmenu: API Methods
title: "pipeline_templates"
navorder: 14
----
+...
h1. pipeline_templates
diff --git a/doc/api/methods/repositories.textile b/doc/api/methods/repositories.textile
index 4137361..3d4aedc 100644
--- a/doc/api/methods/repositories.textile
+++ b/doc/api/methods/repositories.textile
@@ -4,7 +4,7 @@ navsection: api
navmenu: API Methods
title: "repositories"
navorder: 15
----
+...
h1. repositories
diff --git a/doc/api/methods/specimens.textile b/doc/api/methods/specimens.textile
index cf49995..4fa095e 100644
--- a/doc/api/methods/specimens.textile
+++ b/doc/api/methods/specimens.textile
@@ -4,7 +4,7 @@ navsection: api
navmenu: API Methods
title: "specimens"
navorder: 16
----
+...
h1. specimens
diff --git a/doc/api/methods/traits.textile b/doc/api/methods/traits.textile
index 8a8ffcb..28d5678 100644
--- a/doc/api/methods/traits.textile
+++ b/doc/api/methods/traits.textile
@@ -4,7 +4,7 @@ navsection: api
navmenu: API Methods
title: "traits"
navorder: 17
----
+...
h1. traits
diff --git a/doc/api/methods/users.textile b/doc/api/methods/users.textile
index c162133..2ae5eee 100644
--- a/doc/api/methods/users.textile
+++ b/doc/api/methods/users.textile
@@ -4,7 +4,7 @@ navsection: api
navmenu: API Methods
title: "users"
navorder: 18
----
+...
h1. users
diff --git a/doc/api/methods/virtual_machines.textile b/doc/api/methods/virtual_machines.textile
index 3667491..a96fcb4 100644
--- a/doc/api/methods/virtual_machines.textile
+++ b/doc/api/methods/virtual_machines.textile
@@ -4,7 +4,7 @@ navsection: api
navmenu: API Methods
title: "virtual_machines"
navorder: 19
----
+...
h1. virtual_machines
diff --git a/doc/api/permission-model.textile b/doc/api/permission-model.textile
index 843ab25..cc4c0d8 100644
--- a/doc/api/permission-model.textile
+++ b/doc/api/permission-model.textile
@@ -4,7 +4,7 @@ navsection: api
navmenu: Concepts
title: "Permission model"
navorder: 6
----
+...
h1. Permission model
diff --git a/doc/api/resources.textile b/doc/api/resources.textile
index f7c1e69..7247096 100644
--- a/doc/api/resources.textile
+++ b/doc/api/resources.textile
@@ -4,7 +4,7 @@ navsection: api
navmenu: Concepts
title: Resources
navorder: 4
----
+...
h1. Resources
diff --git a/doc/api/schema/ApiClient.textile b/doc/api/schema/ApiClient.textile
index 3d835fb..86f9345 100644
--- a/doc/api/schema/ApiClient.textile
+++ b/doc/api/schema/ApiClient.textile
@@ -4,7 +4,7 @@ navsection: api
navmenu: Schema
title: ApiClient
navorder: 2
----
+...
h1. ApiClient
diff --git a/doc/api/schema/ApiClientAuthorization.textile b/doc/api/schema/ApiClientAuthorization.textile
index 289ff76..d9ee87d 100644
--- a/doc/api/schema/ApiClientAuthorization.textile
+++ b/doc/api/schema/ApiClientAuthorization.textile
@@ -4,7 +4,7 @@ navsection: api
navmenu: Schema
title: ApiClientAuthorization
navorder: 1
----
+...
h1. ApiClientAuthorization
diff --git a/doc/api/schema/AuthorizedKey.textile b/doc/api/schema/AuthorizedKey.textile
index aec56ff..c60ce71 100644
--- a/doc/api/schema/AuthorizedKey.textile
+++ b/doc/api/schema/AuthorizedKey.textile
@@ -4,7 +4,7 @@ navsection: api
navmenu: Schema
title: AuthorizedKey
navorder: 3
----
+...
h1. AuthorizedKey
diff --git a/doc/api/schema/Collection.textile b/doc/api/schema/Collection.textile
index 485ab3c..fb39ff9 100644
--- a/doc/api/schema/Collection.textile
+++ b/doc/api/schema/Collection.textile
@@ -4,7 +4,7 @@ navsection: api
navmenu: Schema
title: Collection
navorder: 4
----
+...
h1. Collection
diff --git a/doc/api/schema/Commit.textile b/doc/api/schema/Commit.textile
index 0a02d8f..71791eb 100644
--- a/doc/api/schema/Commit.textile
+++ b/doc/api/schema/Commit.textile
@@ -4,7 +4,7 @@ navsection: api
navmenu: Schema
title: Commit
navorder: 6
----
+...
h1. Commit
diff --git a/doc/api/schema/CommitAncestor.textile b/doc/api/schema/CommitAncestor.textile
index aac8698..e4788f8 100644
--- a/doc/api/schema/CommitAncestor.textile
+++ b/doc/api/schema/CommitAncestor.textile
@@ -4,7 +4,7 @@ navsection: api
navmenu: Schema
title: CommitAncestor
navorder: 5
----
+...
h1. CommitAncestor
diff --git a/doc/api/schema/Group.textile b/doc/api/schema/Group.textile
index 650cbb7..4315d75 100644
--- a/doc/api/schema/Group.textile
+++ b/doc/api/schema/Group.textile
@@ -4,7 +4,7 @@ navsection: api
navmenu: Schema
title: Group
navorder: 7
----
+...
h1. Group
diff --git a/doc/api/schema/Human.textile b/doc/api/schema/Human.textile
index 596cb0d..31766c9 100644
--- a/doc/api/schema/Human.textile
+++ b/doc/api/schema/Human.textile
@@ -4,7 +4,7 @@ navsection: api
navmenu: Schema
title: Human
navorder: 8
----
+...
h1. Human
diff --git a/doc/api/schema/Job.textile b/doc/api/schema/Job.textile
index 17e7358..631c549 100644
--- a/doc/api/schema/Job.textile
+++ b/doc/api/schema/Job.textile
@@ -4,7 +4,7 @@ navsection: api
navmenu: Schema
title: Job
navorder: 9
----
+...
h1. Job
diff --git a/doc/api/schema/JobTask.textile b/doc/api/schema/JobTask.textile
index 4efaa09..fbbc8ef 100644
--- a/doc/api/schema/JobTask.textile
+++ b/doc/api/schema/JobTask.textile
@@ -4,7 +4,7 @@ navsection: api
navmenu: Schema
title: JobTask
navorder: 10
----
+...
h1. JobTask
diff --git a/doc/api/schema/KeepDisk.textile b/doc/api/schema/KeepDisk.textile
index 152ea8d..d9f36ab 100644
--- a/doc/api/schema/KeepDisk.textile
+++ b/doc/api/schema/KeepDisk.textile
@@ -4,7 +4,7 @@ navsection: api
navmenu: Schema
title: KeepDisk
navorder: 11
----
+...
h1. KeepDisk
diff --git a/doc/api/schema/Link.textile b/doc/api/schema/Link.textile
index ed8271d..05161b3 100644
--- a/doc/api/schema/Link.textile
+++ b/doc/api/schema/Link.textile
@@ -4,7 +4,7 @@ navsection: api
navmenu: Schema
title: Link
navorder: 12
----
+...
h1. Link
diff --git a/doc/api/schema/Log.textile b/doc/api/schema/Log.textile
index b6d1b07..2e86175 100644
--- a/doc/api/schema/Log.textile
+++ b/doc/api/schema/Log.textile
@@ -4,7 +4,7 @@ navsection: api
navmenu: Schema
title: Log
navorder: 14
----
+...
h1. Log
diff --git a/doc/api/schema/Node.textile b/doc/api/schema/Node.textile
index 7a6e4ef..ccdd3e5 100644
--- a/doc/api/schema/Node.textile
+++ b/doc/api/schema/Node.textile
@@ -4,7 +4,7 @@ navsection: api
navmenu: Schema
title: Node
navorder: 15
----
+...
h1. Node
diff --git a/doc/api/schema/PipelineInstance.textile b/doc/api/schema/PipelineInstance.textile
index bdefce2..4eeb989 100644
--- a/doc/api/schema/PipelineInstance.textile
+++ b/doc/api/schema/PipelineInstance.textile
@@ -4,7 +4,7 @@ navsection: api
navmenu: Schema
title: PipelineInstance
navorder: 16
----
+...
h1. PipelineInstance
diff --git a/doc/api/schema/PipelineTemplate.textile b/doc/api/schema/PipelineTemplate.textile
index 8511a49..c54ba58 100644
--- a/doc/api/schema/PipelineTemplate.textile
+++ b/doc/api/schema/PipelineTemplate.textile
@@ -4,7 +4,7 @@ navsection: api
navmenu: Schema
title: PipelineTemplate
navorder: 17
----
+...
h1. PipelineTemplate
diff --git a/doc/api/schema/Repository.textile b/doc/api/schema/Repository.textile
index 084e66e..4989c69 100644
--- a/doc/api/schema/Repository.textile
+++ b/doc/api/schema/Repository.textile
@@ -4,7 +4,7 @@ navsection: api
navmenu: Schema
title: Repository
navorder: 18
----
+...
h1. Repository
diff --git a/doc/api/schema/Specimen.textile b/doc/api/schema/Specimen.textile
index 875c041..04afddc 100644
--- a/doc/api/schema/Specimen.textile
+++ b/doc/api/schema/Specimen.textile
@@ -4,7 +4,7 @@ navsection: api
navmenu: Schema
title: Specimen
navorder: 19
----
+...
h1. Specimen
diff --git a/doc/api/schema/Trait.textile b/doc/api/schema/Trait.textile
index 45087a5..d6829d3 100644
--- a/doc/api/schema/Trait.textile
+++ b/doc/api/schema/Trait.textile
@@ -4,7 +4,7 @@ navsection: api
navmenu: Schema
title: Trait
navorder: 20
----
+...
h1. Trait
diff --git a/doc/api/schema/User.textile b/doc/api/schema/User.textile
index c7fadb3..d141ec0 100644
--- a/doc/api/schema/User.textile
+++ b/doc/api/schema/User.textile
@@ -4,7 +4,7 @@ navsection: api
navmenu: Schema
title: User
navorder: 21
----
+...
h1. User
diff --git a/doc/api/schema/VirtualMachine.textile b/doc/api/schema/VirtualMachine.textile
index 49a23b0..0b5ccb8 100644
--- a/doc/api/schema/VirtualMachine.textile
+++ b/doc/api/schema/VirtualMachine.textile
@@ -4,7 +4,7 @@ navsection: api
navmenu: Schema
title: VirtualMachine
navorder: 22
----
+...
h1. VirtualMachine
diff --git a/doc/index.html b/doc/index.html
index 3ff2956..13c9118 100644
--- a/doc/index.html
+++ b/doc/index.html
@@ -2,7 +2,7 @@
layout: default
navsection: top
title: Arvados | Documentation
----
+...
<div class="frontpagehero">
<div style="padding:100px 50px; margin-left:0px; margin-top:0px">
diff --git a/doc/install/client.textile b/doc/install/client.textile
index 2df30f9..7827a13 100644
--- a/doc/install/client.textile
+++ b/doc/install/client.textile
@@ -3,7 +3,7 @@ layout: default
navsection: installguide
title: Install client libraries
navorder: 5
----
+...
h1. Install client libraries
diff --git a/doc/install/create-standard-objects.textile b/doc/install/create-standard-objects.textile
index 5e34e4e..bbe0fe6 100644
--- a/doc/install/create-standard-objects.textile
+++ b/doc/install/create-standard-objects.textile
@@ -3,7 +3,7 @@ layout: default
navsection: installguide
title: Create standard objects
navorder: 4
----
+...
h1. Create standard objects
diff --git a/doc/install/install-crunch-dispatch.textile b/doc/install/install-crunch-dispatch.textile
index 4c02098..d6525aa 100644
--- a/doc/install/install-crunch-dispatch.textile
+++ b/doc/install/install-crunch-dispatch.textile
@@ -3,7 +3,7 @@ layout: default
navsection: installguide
title: Install the Crunch dispatcher
navorder: 3
----
+...
h1. Crunch setup
diff --git a/doc/user/examples/crunch-examples.textile b/doc/user/examples/crunch-examples.textile
index 6fc9dc0..b1ada1f 100644
--- a/doc/user/examples/crunch-examples.textile
+++ b/doc/user/examples/crunch-examples.textile
@@ -4,7 +4,7 @@ navsection: userguide
navmenu: Examples
title: "Crunch examples"
navorder: 30
----
+...
h1. Crunch examples
diff --git a/doc/user/getting_started/check-environment.textile b/doc/user/getting_started/check-environment.textile
index 298f188..1516c7f 100644
--- a/doc/user/getting_started/check-environment.textile
+++ b/doc/user/getting_started/check-environment.textile
@@ -4,7 +4,7 @@ navsection: userguide
navmenu: Getting Started
title: "Checking your environment"
navorder: 10
----
+...
h1. Checking your environment
diff --git a/doc/user/getting_started/ssh-access.textile b/doc/user/getting_started/ssh-access.textile
index 59f976f..1803b56 100644
--- a/doc/user/getting_started/ssh-access.textile
+++ b/doc/user/getting_started/ssh-access.textile
@@ -4,7 +4,7 @@ navsection: userguide
navmenu: Getting Started
title: Accessing an Arvados VM over ssh
navorder: 2
----
+...
h1. Accessing an Arvados Virtual Machine over ssh
diff --git a/doc/user/getting_started/workbench.textile b/doc/user/getting_started/workbench.textile
index cbe0e35..2b72cd3 100644
--- a/doc/user/getting_started/workbench.textile
+++ b/doc/user/getting_started/workbench.textile
@@ -4,7 +4,7 @@ navsection: userguide
navmenu: Getting Started
title: Accessing Arvados Workbench
navorder: 1
----
+...
h1. Accessing Arvados Workbench
Access the Arvados beta test instance available using this link:
diff --git a/doc/user/index.textile b/doc/user/index.textile
index 085f6be..cc723f6 100644
--- a/doc/user/index.textile
+++ b/doc/user/index.textile
@@ -3,7 +3,7 @@ layout: default
navsection: userguide
title: Welcome to Arvados!
navorder: 0
----
+...
h1. Welcome to Arvados!
diff --git a/doc/user/reference/api-tokens.textile b/doc/user/reference/api-tokens.textile
index 928ba26..b3938f2 100644
--- a/doc/user/reference/api-tokens.textile
+++ b/doc/user/reference/api-tokens.textile
@@ -4,7 +4,7 @@ navsection: userguide
navmenu: Reference
title: "Getting an API token"
navorder: 01
----
+...
h1. Reference: Getting an API token
diff --git a/doc/user/reference/crunch-utility-libraries.textile b/doc/user/reference/crunch-utility-libraries.textile
index 524040f..679138d 100644
--- a/doc/user/reference/crunch-utility-libraries.textile
+++ b/doc/user/reference/crunch-utility-libraries.textile
@@ -4,7 +4,7 @@ navsection: userguide
navmenu: Reference
title: "Crunch utility libraries"
navorder: 31
----
+...
h1. Crunch utility libraries
diff --git a/doc/user/reference/sdk-cli.textile b/doc/user/reference/sdk-cli.textile
index 706fe93..fd8e86d 100644
--- a/doc/user/reference/sdk-cli.textile
+++ b/doc/user/reference/sdk-cli.textile
@@ -4,7 +4,7 @@ navsection: userguide
navmenu: Reference
title: "Command line SDK"
navorder: 22
----
+...
h1. Reference: Command line SDK
diff --git a/doc/user/reference/sdk-python.textile b/doc/user/reference/sdk-python.textile
index 29212c1..d9b1e5d 100644
--- a/doc/user/reference/sdk-python.textile
+++ b/doc/user/reference/sdk-python.textile
@@ -4,7 +4,7 @@ navsection: userguide
navmenu: Reference
title: "Python SDK"
navorder: 23
----
+...
h1. Reference: Python SDK
diff --git a/doc/user/tutorials/tutorial-firstscript.textile b/doc/user/tutorials/tutorial-firstscript.textile
index bfde02c..b03aaa3 100644
--- a/doc/user/tutorials/tutorial-firstscript.textile
+++ b/doc/user/tutorials/tutorial-firstscript.textile
@@ -4,7 +4,7 @@ navsection: userguide
navmenu: Tutorials
title: "Writing a Crunch script"
navorder: 13
----
+...
h1. Tutorial: Writing a Crunch script
diff --git a/doc/user/tutorials/tutorial-gatk-variantfiltration.textile b/doc/user/tutorials/tutorial-gatk-variantfiltration.textile
index 77306d0..5e985c8 100644
--- a/doc/user/tutorials/tutorial-gatk-variantfiltration.textile
+++ b/doc/user/tutorials/tutorial-gatk-variantfiltration.textile
@@ -4,7 +4,7 @@ navsection: userguide
navmenu: Tutorials
title: "Using GATK with Arvados"
navorder: 16
----
+...
h1. Tutorial: Using GATK with Arvados
diff --git a/doc/user/tutorials/tutorial-job-debug.textile b/doc/user/tutorials/tutorial-job-debug.textile
index 9ea454c..ad01eaa 100644
--- a/doc/user/tutorials/tutorial-job-debug.textile
+++ b/doc/user/tutorials/tutorial-job-debug.textile
@@ -4,7 +4,7 @@ navsection: userguide
navmenu: Tutorials
title: "Debugging a Crunch script"
navorder: 14
----
+...
h1. Tutorial: Debugging a Crunch script
diff --git a/doc/user/tutorials/tutorial-job1.textile b/doc/user/tutorials/tutorial-job1.textile
index 253c4bd..f920019 100644
--- a/doc/user/tutorials/tutorial-job1.textile
+++ b/doc/user/tutorials/tutorial-job1.textile
@@ -4,7 +4,7 @@ navsection: userguide
navmenu: Tutorials
title: "Running a Crunch job"
navorder: 12
----
+...
h1. Tutorial: Running a crunch job
diff --git a/doc/user/tutorials/tutorial-keep.textile b/doc/user/tutorials/tutorial-keep.textile
index 8255440..2220ce1 100644
--- a/doc/user/tutorials/tutorial-keep.textile
+++ b/doc/user/tutorials/tutorial-keep.textile
@@ -4,7 +4,7 @@ navsection: userguide
navmenu: Tutorials
title: "Storing and Retrieving data using Arvados Keep"
navorder: 11
----
+...
h1. Tutorial: Storing and Retrieving data using Arvados Keep
diff --git a/doc/user/tutorials/tutorial-new-pipeline.textile b/doc/user/tutorials/tutorial-new-pipeline.textile
index 5277bfc..3eb9796 100644
--- a/doc/user/tutorials/tutorial-new-pipeline.textile
+++ b/doc/user/tutorials/tutorial-new-pipeline.textile
@@ -4,7 +4,7 @@ navsection: userguide
navmenu: Tutorials
title: "Constructing a Crunch pipeline"
navorder: 15
----
+...
h1. Tutorial: Constructing a Crunch pipeline
diff --git a/doc/user/tutorials/tutorial-parallel.textile b/doc/user/tutorials/tutorial-parallel.textile
index 149da77..3f278a7 100644
--- a/doc/user/tutorials/tutorial-parallel.textile
+++ b/doc/user/tutorials/tutorial-parallel.textile
@@ -4,7 +4,7 @@ navsection: userguide
navmenu: Tutorials
title: "Parallel Crunch tasks"
navorder: 15
----
+...
h1. Tutorial: Parallel Crunch tasks
diff --git a/doc/user/tutorials/tutorial-trait-search.textile b/doc/user/tutorials/tutorial-trait-search.textile
index 4f4ec9c..89492d2 100644
--- a/doc/user/tutorials/tutorial-trait-search.textile
+++ b/doc/user/tutorials/tutorial-trait-search.textile
@@ -4,7 +4,7 @@ navsection: userguide
navmenu: Tutorials
title: "Querying the Metadata Database"
navorder: 16
----
+...
h1. Tutorial: Querying the Metadata Database
commit 68ad3cbe4aaaa986b5b6e9f5cfcbf9d9d4c1c319
Author: Peter Amstutz <peter.amstutz at curoverse.com>
Date: Tue Dec 31 16:49:42 2013 -0500
Started tinkering with zenweb
diff --git a/doc/Gemfile b/doc/Gemfile
index a9cccb4..ea40d14 100644
--- a/doc/Gemfile
+++ b/doc/Gemfile
@@ -1,4 +1,4 @@
source 'https://rubygems.org'
-gem 'jekyll'
-gem 'RedCloth'
+gem 'zenweb'
+gem 'zenweb-textile'
diff --git a/doc/Gemfile.lock b/doc/Gemfile.lock
index 80a5619..608a001 100644
--- a/doc/Gemfile.lock
+++ b/doc/Gemfile.lock
@@ -2,48 +2,27 @@ GEM
remote: https://rubygems.org/
specs:
RedCloth (4.2.9)
- classifier (1.3.3)
- fast-stemmer (>= 1.0.0)
- colorator (0.1)
- commander (4.1.5)
- highline (~> 1.6.11)
- fast-stemmer (1.0.2)
- ffi (1.9.3)
- highline (1.6.20)
- jekyll (1.3.0)
- classifier (~> 1.3)
- colorator (~> 0.1)
- commander (~> 4.1.3)
- liquid (~> 2.5.2)
- listen (~> 1.3)
- maruku (~> 0.6.0)
- pygments.rb (~> 0.5.0)
- redcarpet (~> 2.3.0)
- safe_yaml (~> 0.9.7)
- liquid (2.5.4)
- listen (1.3.1)
- rb-fsevent (>= 0.9.3)
- rb-inotify (>= 0.9)
- rb-kqueue (>= 0.2)
- maruku (0.6.1)
- syntax (>= 1.0.0)
- posix-spawn (0.3.6)
- pygments.rb (0.5.4)
- posix-spawn (~> 0.3.6)
- yajl-ruby (~> 1.1.0)
- rb-fsevent (0.9.3)
- rb-inotify (0.9.2)
- ffi (>= 0.5.0)
- rb-kqueue (0.2.0)
- ffi (>= 0.5.0)
- redcarpet (2.3.0)
- safe_yaml (0.9.7)
- syntax (1.0.0)
- yajl-ruby (1.1.0)
+ coderay (1.1.0)
+ kramdown (0.14.2)
+ less (1.2.21)
+ mutter (>= 0.4.2)
+ treetop (>= 1.4.2)
+ mutter (0.5.3)
+ polyglot (0.3.3)
+ treetop (1.4.15)
+ polyglot
+ polyglot (>= 0.3.1)
+ zenweb (3.0.0.b3)
+ coderay (~> 1.0)
+ kramdown (~> 0.13)
+ less (~> 1.2)
+ zenweb-textile (0.0.1)
+ RedCloth (~> 4.2.9)
+ zenweb (= 3.0.0.b3)
PLATFORMS
ruby
DEPENDENCIES
- RedCloth
- jekyll
+ zenweb
+ zenweb-textile
diff --git a/doc/README_FOR_APP b/doc/README_FOR_APP
deleted file mode 100644
index fe41f5c..0000000
--- a/doc/README_FOR_APP
+++ /dev/null
@@ -1,2 +0,0 @@
-Use this README file to introduce your application and point to useful places in the API for learning more.
-Run "rake doc:app" to generate API documentation for your models, controllers, helpers, and libraries.
diff --git a/doc/Rakefile b/doc/Rakefile
new file mode 100755
index 0000000..12f87b1
--- /dev/null
+++ b/doc/Rakefile
@@ -0,0 +1,6 @@
+#!/usr/bin/env rake
+
+require "rubygems"
+require "zenweb/tasks"
+load "zenweb-textile.rb"
+
diff --git a/doc/_config.yml b/doc/_config.yml
index a4fed53..108ec24 100644
--- a/doc/_config.yml
+++ b/doc/_config.yml
@@ -1,3 +1,4 @@
+exclude: ["Rakefile", "tmp"]
baseurl: /doc
arvados_api_host: qr1hi.arvadosapi.com
navbar:
diff --git a/doc/zenweb-textile.rb b/doc/zenweb-textile.rb
new file mode 100644
index 0000000..bdd7162
--- /dev/null
+++ b/doc/zenweb-textile.rb
@@ -0,0 +1,23 @@
+require 'zenweb'
+
+module ZenwebTextile
+ VERSION = '0.0.1'
+end
+
+module Zenweb
+ class Page
+
+ ##
+ # Render a page's textile and return the resulting html
+ def render_textile page, content
+ textile body
+ end
+
+ ##
+ # Render textile in +content+
+ def textile content
+ require 'RedCloth'
+ @textile = RedCloth.new(content).to_html
+ end
+ end
+end
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