[ARVADOS] updated: 296a8cba6b65654156d3ff3abc07522a4824935e
git at public.curoverse.com
git at public.curoverse.com
Thu Mar 20 15:02:13 EDT 2014
Summary of changes:
doc/README | 5 +-
doc/_config.yml | 1 +
doc/_includes/_webring.liquid | 6 +-
doc/api/schema/ApiClient.html.textile.liquid | 4 +-
.../ApiClientAuthorization.html.textile.liquid | 2 +-
doc/api/schema/AuthorizedKey.html.textile.liquid | 5 +-
doc/api/schema/Collection.html.textile.liquid | 6 +-
doc/api/schema/Commit.html.textile.liquid | 4 +-
doc/api/schema/CommitAncestor.html.textile.liquid | 4 +-
doc/api/schema/Group.html.textile.liquid | 4 +-
doc/api/schema/Human.html.textile.liquid | 4 +-
doc/api/schema/Job.html.textile.liquid | 6 +-
doc/api/schema/JobTask.html.textile.liquid | 4 +-
doc/api/schema/KeepDisk.html.textile.liquid | 4 +-
doc/api/schema/Link.html.textile.liquid | 4 +-
doc/api/schema/Log.html.textile.liquid | 4 +-
doc/api/schema/Node.html.textile.liquid | 4 +-
.../schema/PipelineInstance.html.textile.liquid | 4 +-
.../schema/PipelineTemplate.html.textile.liquid | 4 +-
doc/api/schema/Repository.html.textile.liquid | 4 +-
doc/api/schema/Specimen.html.textile.liquid | 4 +-
doc/api/schema/Trait.html.textile.liquid | 4 +-
doc/api/schema/User.html.textile.liquid | 4 +-
doc/api/schema/VirtualMachine.html.textile.liquid | 4 +-
doc/gen_api_schema_docs.py | 3 +-
doc/index.html.liquid | 2 +-
doc/user/copying/agpl-3.0.html | 2 +-
.../job-and-pipeline-reference.html.textile.liquid | 223 ++++++++++++++++++++
doc/user/topics/keep.html.textile.liquid | 2 +-
...nning-pipeline-command-line.html.textile.liquid | 7 +-
...rial-gatk-variantfiltration.html.textile.liquid | 1 +
doc/user/topics/tutorial-job1.html.textile.liquid | 12 +-
.../topics/tutorial-parallel.html.textile.liquid | 3 +-
.../running-external-program.html.textile.liquid | 5 +-
.../tutorial-firstscript.html.textile.liquid | 10 +-
.../tutorial-new-pipeline.html.textile.liquid | 8 +-
...tutorial-pipeline-workbench.html.textile.liquid | 4 +-
37 files changed, 307 insertions(+), 74 deletions(-)
create mode 100644 doc/user/reference/job-and-pipeline-reference.html.textile.liquid
via 296a8cba6b65654156d3ff3abc07522a4824935e (commit)
via 127f1e032068d83365d783e8fe8cad5f0117638a (commit)
from 620bcbd5734e860a1e67bb85e4899233bc4a6b28 (commit)
Those revisions listed above that are new to this repository have
not appeared on any other notification email; so we list those
revisions in full, below.
commit 296a8cba6b65654156d3ff3abc07522a4824935e
Author: Peter Amstutz <peter.amstutz at curoverse.com>
Date: Thu Mar 20 15:02:09 2014 -0400
Documentation fixes based on running linkchecker.
diff --git a/doc/README b/doc/README
index e7bd431..e7e7a21 100644
--- a/doc/README
+++ b/doc/README
@@ -18,11 +18,14 @@ Arvados Documentation
Then go to http://localhost:8000
-2. You can set 'baseurl' (the URL prefix for all internal links),
+3. You can set 'baseurl' (the URL prefix for all internal links),
'arvados_api_host' and 'arvados_workbench_host' without changing _config.yml:
$ rake generate baseurl=/example arvados_api_host=example.com
+To use file:/// links:
+
+ $ rake baseurl=$PWD/.site
4. To delete generated files:
$ rake realclean
diff --git a/doc/_config.yml b/doc/_config.yml
index 8d4fd5e..b48d714 100644
--- a/doc/_config.yml
+++ b/doc/_config.yml
@@ -40,6 +40,7 @@ navbar:
- Reference:
- user/reference/api-tokens.html.textile.liquid
- user/reference/sdk-cli.html.textile.liquid
+ - user/reference/job-and-pipeline-reference.html.textile.liquid
- Arvados License:
- user/copying/copying.html.textile.liquid
- user/copying/agpl-3.0.html
diff --git a/doc/_includes/_webring.liquid b/doc/_includes/_webring.liquid
index edcfedf..7cb9468 100644
--- a/doc/_includes/_webring.liquid
+++ b/doc/_includes/_webring.liquid
@@ -8,9 +8,9 @@
{% if nx == 1 %}
<hr>
{% if prev != "" %}
- <a href="{{ site.baseurl }}{{ prev.url }}" class="pull-left">Previous: {{ prev.title }}</a></li>
+ <a href="{{ site.baseurl }}{{ prev.url }}" class="pull-left">Previous: {{ prev.title }}</a>
{% endif %}
- <a href="{{ site.baseurl }}{{ p.url }}" class="pull-right">Next: {{ p.title }}</a></li>
+ <a href="{{ site.baseurl }}{{ p.url }}" class="pull-right">Next: {{ p.title }}</a>
{% assign nx = 0 %}
{% assign n = 1 %}
{% endif %}
@@ -24,6 +24,6 @@
{% endfor %}
{% if n == 0 && prev != "" %}
<hr>
- <a href="{{ site.baseurl }}{{ prev.url }}" class="pull-left">Previous: {{ prev.title }}</a></li>
+ <a href="{{ site.baseurl }}{{ prev.url }}" class="pull-left">Previous: {{ prev.title }}</a>
{% assign n = 1 %}
{% endif %}
\ No newline at end of file
diff --git a/doc/api/schema/ApiClient.html.textile.liquid b/doc/api/schema/ApiClient.html.textile.liquid
index 402d9ab..914537d 100644
--- a/doc/api/schema/ApiClient.html.textile.liquid
+++ b/doc/api/schema/ApiClient.html.textile.liquid
@@ -13,7 +13,7 @@ An **ApiClient** represents a client program that has issued a request to the AP
h2. Methods
-See "REST methods for working with Arvados resources":/api/methods.html
+See "REST methods for working with Arvados resources":{{site.baseurl}}/api/methods.html
API endpoint base: @https://{{ site.arvados_api_host }}/arvados/v1/api_clients@
@@ -29,7 +29,7 @@ Side effects of creating an ApiClient.
h2. Resources
-Each ApiClient has, in addition to the usual "attributes of Arvados resources":/api/resources.html:
+Each ApiClient has, in addition to the usual "attributes of Arvados resources":{{site.baseurl}}/api/resources.html:
table(table table-bordered table-condensed).
|_. Attribute|_. Type|_. Description|_. Example|
diff --git a/doc/api/schema/ApiClientAuthorization.html.textile.liquid b/doc/api/schema/ApiClientAuthorization.html.textile.liquid
index 2c0945b..d4bbd59 100644
--- a/doc/api/schema/ApiClientAuthorization.html.textile.liquid
+++ b/doc/api/schema/ApiClientAuthorization.html.textile.liquid
@@ -12,7 +12,7 @@ A **ApiClientAuthorization** represents the API authorization token that has bee
h2. Methods
-See "REST methods for working with Arvados resources":/api/methods.html
+See "REST methods for working with Arvados resources":{{site.baseurl}}/api/methods.html
API endpoint base: @https://{{ site.arvados_api_host }}/arvados/v1/api_client_authorizations@
diff --git a/doc/api/schema/AuthorizedKey.html.textile.liquid b/doc/api/schema/AuthorizedKey.html.textile.liquid
index cb3443d..f3dd847 100644
--- a/doc/api/schema/AuthorizedKey.html.textile.liquid
+++ b/doc/api/schema/AuthorizedKey.html.textile.liquid
@@ -3,7 +3,6 @@ layout: default
navsection: api
navmenu: Schema
title: AuthorizedKey
-
...
@@ -12,7 +11,7 @@ A **AuthorizedKey** represents...
h2. Methods
-See "REST methods for working with Arvados resources":/api/methods.html
+See "REST methods for working with Arvados resources":{{site.baseurl}}/api/methods.html
API endpoint base: @https://{{ site.arvados_api_host }}/arvados/v1/authorized_keys@
@@ -28,7 +27,7 @@ Side effects of creating a AuthorizedKey.
h2. Resources
-Each AuthorizedKey has, in addition to the usual "attributes of Arvados resources":/api/resources.html:
+Each AuthorizedKey has, in addition to the usual "attributes of Arvados resources":{{site.baseurl}}/api/resources.html:
table(table table-bordered table-condensed).
|_. Attribute|_. Type|_. Description|_. Example|
diff --git a/doc/api/schema/Collection.html.textile.liquid b/doc/api/schema/Collection.html.textile.liquid
index ff08d81..2aa558a 100644
--- a/doc/api/schema/Collection.html.textile.liquid
+++ b/doc/api/schema/Collection.html.textile.liquid
@@ -8,12 +8,12 @@ title: Collection
-This resource concerns metadata, usage accounting, and integrity checks for data stored on the cloud. Reading and writing the data _per se_ is achieved by the "Keep":/user/tutorials/tutorial-keep.html storage system.
+This resource concerns metadata, usage accounting, and integrity checks for data stored on the cloud. Reading and writing the data _per se_ is achieved by the "Keep":{{site.baseurl}}/user/tutorials/tutorial-keep.html storage system.
h2. Methods
-See "REST methods for working with Arvados resources":/api/methods.html
+See "REST methods for working with Arvados resources":{{site.baseurl}}/api/methods.html
API endpoint base: @https://{{ site.arvados_api_host }}/arvados/v1/links@
@@ -31,7 +31,7 @@ Clients can request checks of data integrity and storage redundancy.
h2. Resource
-Each collection has, in addition to the usual "attributes of Arvados resources":/api/resources.html:
+Each collection has, in addition to the usual "attributes of Arvados resources":{{site.baseurl}}/api/resources.html:
table(table table-bordered table-condensed).
|_. Attribute|_. Type|_. Description|_. Example|
diff --git a/doc/api/schema/Commit.html.textile.liquid b/doc/api/schema/Commit.html.textile.liquid
index 0c33859..36de53f 100644
--- a/doc/api/schema/Commit.html.textile.liquid
+++ b/doc/api/schema/Commit.html.textile.liquid
@@ -12,7 +12,7 @@ A **Commit** represents...
h2. Methods
-See "REST methods for working with Arvados resources":/api/methods.html
+See "REST methods for working with Arvados resources":{{site.baseurl}}/api/methods.html
API endpoint base: @https://{{ site.arvados_api_host }}/arvados/v1/commits@
@@ -28,7 +28,7 @@ Side effects of creating a Commit.
h2. Resources
-Each Commit has, in addition to the usual "attributes of Arvados resources":/api/resources.html:
+Each Commit has, in addition to the usual "attributes of Arvados resources":{{site.baseurl}}/api/resources.html:
table(table table-bordered table-condensed).
|_. Attribute|_. Type|_. Description|_. Example|
diff --git a/doc/api/schema/CommitAncestor.html.textile.liquid b/doc/api/schema/CommitAncestor.html.textile.liquid
index c1bc472..b488785 100644
--- a/doc/api/schema/CommitAncestor.html.textile.liquid
+++ b/doc/api/schema/CommitAncestor.html.textile.liquid
@@ -12,7 +12,7 @@ A **CommitAncestor** represents...
h2. Methods
-See "REST methods for working with Arvados resources":/api/methods.html
+See "REST methods for working with Arvados resources":{{site.baseurl}}/api/methods.html
API endpoint base: @https://{{ site.arvados_api_host }}/arvados/v1/commit_ancestors@
@@ -28,7 +28,7 @@ Side effects of creating a CommitAncestor.
h2. Resources
-Each CommitAncestor has, in addition to the usual "attributes of Arvados resources":/api/resources.html:
+Each CommitAncestor has, in addition to the usual "attributes of Arvados resources":{{site.baseurl}}/api/resources.html:
table(table table-bordered table-condensed).
|_. Attribute|_. Type|_. Description|_. Example|
diff --git a/doc/api/schema/Group.html.textile.liquid b/doc/api/schema/Group.html.textile.liquid
index 607e26b..e0e092e 100644
--- a/doc/api/schema/Group.html.textile.liquid
+++ b/doc/api/schema/Group.html.textile.liquid
@@ -12,7 +12,7 @@ A **Group** represents...
h2. Methods
-See "REST methods for working with Arvados resources":/api/methods.html
+See "REST methods for working with Arvados resources":{{site.baseurl}}/api/methods.html
API endpoint base: @https://{{ site.arvados_api_host }}/arvados/v1/groups@
@@ -28,7 +28,7 @@ Side effects of creating a Group.
h2. Resources
-Each Group has, in addition to the usual "attributes of Arvados resources":/api/resources.html:
+Each Group has, in addition to the usual "attributes of Arvados resources":{{site.baseurl}}/api/resources.html:
table(table table-bordered table-condensed).
|_. Attribute|_. Type|_. Description|_. Example|
diff --git a/doc/api/schema/Human.html.textile.liquid b/doc/api/schema/Human.html.textile.liquid
index 5ddb6e4..66bc5f1 100644
--- a/doc/api/schema/Human.html.textile.liquid
+++ b/doc/api/schema/Human.html.textile.liquid
@@ -12,7 +12,7 @@ A **Human** represents...
h2. Methods
-See "REST methods for working with Arvados resources":/api/methods.html
+See "REST methods for working with Arvados resources":{{site.baseurl}}/api/methods.html
API endpoint base: @https://{{ site.arvados_api_host }}/arvados/v1/humans@
@@ -28,7 +28,7 @@ Side effects of creating a Human.
h2. Resources
-Each Human has, in addition to the usual "attributes of Arvados resources":/api/resources.html:
+Each Human has, in addition to the usual "attributes of Arvados resources":{{site.baseurl}}/api/resources.html:
table(table table-bordered table-condensed).
|_. Attribute|_. Type|_. Description|_. Example|
diff --git a/doc/api/schema/Job.html.textile.liquid b/doc/api/schema/Job.html.textile.liquid
index 77579ff..47f8785 100644
--- a/doc/api/schema/Job.html.textile.liquid
+++ b/doc/api/schema/Job.html.textile.liquid
@@ -15,7 +15,7 @@ Applications submit compute jobs when:
h2. Methods
-See "REST methods for working with Arvados resources":/api/methods.html
+See "REST methods for working with Arvados resources":{{site.baseurl}}/api/methods.html
API endpoint base: @https://{{ site.arvados_api_host }}/arvados/v1/jobs@
@@ -37,11 +37,11 @@ where[owner_uuid]=xyzzy-tpzed-a4lcehql0dv2u25
→ Job resource list
-This method is equivalent to the "index method":/api/methods.html#index, except that the results are restricted to queued jobs (i.e., jobs that have not yet been started or cancelled) and order defaults to queue priority.
+This method is equivalent to the "index method":{{site.baseurl}}/api/methods.html#index, except that the results are restricted to queued jobs (i.e., jobs that have not yet been started or cancelled) and order defaults to queue priority.
h2. Resource
-Each job has, in addition to the usual "attributes of Arvados resources":/api/resources.html:
+Each job has, in addition to the usual "attributes of Arvados resources":{{site.baseurl}}/api/resources.html:
table(table table-bordered table-condensed).
|_. Attribute|_. Type|_. Description|_. Notes|
diff --git a/doc/api/schema/JobTask.html.textile.liquid b/doc/api/schema/JobTask.html.textile.liquid
index 4e7aee9..67c16ff 100644
--- a/doc/api/schema/JobTask.html.textile.liquid
+++ b/doc/api/schema/JobTask.html.textile.liquid
@@ -22,13 +22,13 @@ Job tasks have particular update semantics:
h2. Methods
-See "REST methods for working with Arvados resources":/api/methods.html
+See "REST methods for working with Arvados resources":{{site.baseurl}}/api/methods.html
API endpoint base: @https://{{ site.arvados_api_host }}/arvados/v1/job_tasks@
h2. Resources
-Each JobTask has, in addition to the usual "attributes of Arvados resources":/api/resources.html:
+Each JobTask has, in addition to the usual "attributes of Arvados resources":{{site.baseurl}}/api/resources.html:
table(table table-bordered table-condensed).
|_. Attribute|_. Type|_. Description|_. Example|
diff --git a/doc/api/schema/KeepDisk.html.textile.liquid b/doc/api/schema/KeepDisk.html.textile.liquid
index abfb368..8779b1f 100644
--- a/doc/api/schema/KeepDisk.html.textile.liquid
+++ b/doc/api/schema/KeepDisk.html.textile.liquid
@@ -12,7 +12,7 @@ A **KeepDisk** represents...
h2. Methods
-See "REST methods for working with Arvados resources":/api/methods.html
+See "REST methods for working with Arvados resources":{{site.baseurl}}/api/methods.html
API endpoint base: @https://{{ site.arvados_api_host }}/arvados/v1/keep_disks@
@@ -28,7 +28,7 @@ Side effects of creating a KeepDisk.
h2. Resources
-Each KeepDisk has, in addition to the usual "attributes of Arvados resources":/api/resources.html:
+Each KeepDisk has, in addition to the usual "attributes of Arvados resources":{{site.baseurl}}/api/resources.html:
table(table table-bordered table-condensed).
|_. Attribute|_. Type|_. Description|_. Example|
diff --git a/doc/api/schema/Link.html.textile.liquid b/doc/api/schema/Link.html.textile.liquid
index 1191f87..3556055 100644
--- a/doc/api/schema/Link.html.textile.liquid
+++ b/doc/api/schema/Link.html.textile.liquid
@@ -16,13 +16,13 @@ For links that don't make sense to share between API clients, a _link_class_ tha
h2. Methods
-See "REST methods for working with Arvados resources":/api/methods.html
+See "REST methods for working with Arvados resources":{{site.baseurl}}/api/methods.html
API endpoint base: @https://{{ site.arvados_api_host }}/arvados/v1/links@
h2. Resource
-Each link has, in addition to the usual "attributes of Arvados resources":/api/resources.html:
+Each link has, in addition to the usual "attributes of Arvados resources":{{site.baseurl}}/api/resources.html:
table(table table-bordered table-condensed).
|_. Attribute|_. Type|_. Description|
diff --git a/doc/api/schema/Log.html.textile.liquid b/doc/api/schema/Log.html.textile.liquid
index c9530f4..3f00339 100644
--- a/doc/api/schema/Log.html.textile.liquid
+++ b/doc/api/schema/Log.html.textile.liquid
@@ -12,7 +12,7 @@ title: Log
h2. Methods
-See "REST methods for working with Arvados resources":/api/methods.html
+See "REST methods for working with Arvados resources":{{site.baseurl}}/api/methods.html
API endpoint base: @https://{{ site.arvados_api_host }}/arvados/v1/logs@
@@ -26,7 +26,7 @@ At the time of this writing, the Arvados system uses Logs only to record interac
h2. Resources
-Each Log has, in addition to the usual "attributes of Arvados resources":/api/resources.html:
+Each Log has, in addition to the usual "attributes of Arvados resources":{{site.baseurl}}/api/resources.html:
table(table table-bordered table-condensed).
|_. Attribute|_. Type|_. Description|_. Example|
diff --git a/doc/api/schema/Node.html.textile.liquid b/doc/api/schema/Node.html.textile.liquid
index a067fbe..6a4331a 100644
--- a/doc/api/schema/Node.html.textile.liquid
+++ b/doc/api/schema/Node.html.textile.liquid
@@ -12,7 +12,7 @@ A **Node** represents...
h2. Methods
-See "REST methods for working with Arvados resources":/api/methods.html
+See "REST methods for working with Arvados resources":{{site.baseurl}}/api/methods.html
API endpoint base: @https://{{ site.arvados_api_host }}/arvados/v1/nodes@
@@ -28,7 +28,7 @@ Side effects of creating a Node.
h2. Resources
-Each Node has, in addition to the usual "attributes of Arvados resources":/api/resources.html:
+Each Node has, in addition to the usual "attributes of Arvados resources":{{site.baseurl}}/api/resources.html:
table(table table-bordered table-condensed).
|_. Attribute|_. Type|_. Description|_. Example|
diff --git a/doc/api/schema/PipelineInstance.html.textile.liquid b/doc/api/schema/PipelineInstance.html.textile.liquid
index ecb9520..bd1009d 100644
--- a/doc/api/schema/PipelineInstance.html.textile.liquid
+++ b/doc/api/schema/PipelineInstance.html.textile.liquid
@@ -12,7 +12,7 @@ A **PipelineInstance** represents...
h2. Methods
-See "REST methods for working with Arvados resources":/api/methods.html
+See "REST methods for working with Arvados resources":{{site.baseurl}}/api/methods.html
API endpoint base: @https://{{ site.arvados_api_host }}/arvados/v1/pipeline_instances@
@@ -28,7 +28,7 @@ Side effects of creating a PipelineInstance.
h2. Resources
-Each PipelineInstance has, in addition to the usual "attributes of Arvados resources":/api/resources.html:
+Each PipelineInstance has, in addition to the usual "attributes of Arvados resources":{{site.baseurl}}/api/resources.html:
table(table table-bordered table-condensed).
|_. Attribute|_. Type|_. Description|_. Example|
diff --git a/doc/api/schema/PipelineTemplate.html.textile.liquid b/doc/api/schema/PipelineTemplate.html.textile.liquid
index d100c06..c8681c3 100644
--- a/doc/api/schema/PipelineTemplate.html.textile.liquid
+++ b/doc/api/schema/PipelineTemplate.html.textile.liquid
@@ -12,7 +12,7 @@ A **PipelineTemplate** represents...
h2. Methods
-See "REST methods for working with Arvados resources":/api/methods.html
+See "REST methods for working with Arvados resources":{{site.baseurl}}/api/methods.html
API endpoint base: @https://{{ site.arvados_api_host }}/arvados/v1/pipeline_templates@
@@ -28,7 +28,7 @@ Side effects of creating a PipelineTemplate.
h2. Resources
-Each PipelineTemplate has, in addition to the usual "attributes of Arvados resources":/api/resources.html:
+Each PipelineTemplate has, in addition to the usual "attributes of Arvados resources":{{site.baseurl}}/api/resources.html:
table(table table-bordered table-condensed).
|_. Attribute|_. Type|_. Description|_. Example|
diff --git a/doc/api/schema/Repository.html.textile.liquid b/doc/api/schema/Repository.html.textile.liquid
index 8c751d7..7c23eff 100644
--- a/doc/api/schema/Repository.html.textile.liquid
+++ b/doc/api/schema/Repository.html.textile.liquid
@@ -12,7 +12,7 @@ A **Repository** represents...
h2. Methods
-See "REST methods for working with Arvados resources":/api/methods.html
+See "REST methods for working with Arvados resources":{{site.baseurl}}/api/methods.html
API endpoint base: @https://{{ site.arvados_api_host }}/arvados/v1/repositories@
@@ -28,7 +28,7 @@ Side effects of creating a Repository.
h2. Resources
-Each Repository has, in addition to the usual "attributes of Arvados resources":/api/resources.html:
+Each Repository has, in addition to the usual "attributes of Arvados resources":{{site.baseurl}}/api/resources.html:
table(table table-bordered table-condensed).
|_. Attribute|_. Type|_. Description|_. Example|
diff --git a/doc/api/schema/Specimen.html.textile.liquid b/doc/api/schema/Specimen.html.textile.liquid
index f841f0e..4add1a4 100644
--- a/doc/api/schema/Specimen.html.textile.liquid
+++ b/doc/api/schema/Specimen.html.textile.liquid
@@ -12,7 +12,7 @@ A **Specimen** represents...
h2. Methods
-See "REST methods for working with Arvados resources":/api/methods.html
+See "REST methods for working with Arvados resources":{{site.baseurl}}/api/methods.html
API endpoint base: @https://{{ site.arvados_api_host }}/arvados/v1/specimens@
@@ -28,7 +28,7 @@ Side effects of creating a Specimen.
h2. Resources
-Each Specimen has, in addition to the usual "attributes of Arvados resources":/api/resources.html:
+Each Specimen has, in addition to the usual "attributes of Arvados resources":{{site.baseurl}}/api/resources.html:
table(table table-bordered table-condensed).
|_. Attribute|_. Type|_. Description|_. Example|
diff --git a/doc/api/schema/Trait.html.textile.liquid b/doc/api/schema/Trait.html.textile.liquid
index d35cebe..fcb9756 100644
--- a/doc/api/schema/Trait.html.textile.liquid
+++ b/doc/api/schema/Trait.html.textile.liquid
@@ -12,7 +12,7 @@ A **Trait** represents...
h2. Methods
-See "REST methods for working with Arvados resources":/api/methods.html
+See "REST methods for working with Arvados resources":{{site.baseurl}}/api/methods.html
API endpoint base: @https://{{ site.arvados_api_host }}/arvados/v1/traits@
@@ -28,7 +28,7 @@ Side effects of creating a Trait.
h2. Resources
-Each Trait has, in addition to the usual "attributes of Arvados resources":/api/resources.html:
+Each Trait has, in addition to the usual "attributes of Arvados resources":{{site.baseurl}}/api/resources.html:
table(table table-bordered table-condensed).
|_. Attribute|_. Type|_. Description|_. Example|
diff --git a/doc/api/schema/User.html.textile.liquid b/doc/api/schema/User.html.textile.liquid
index a75cf7e..461147c 100644
--- a/doc/api/schema/User.html.textile.liquid
+++ b/doc/api/schema/User.html.textile.liquid
@@ -12,7 +12,7 @@ A **User** represents...
h2. Methods
-See "REST methods for working with Arvados resources":/api/methods.html
+See "REST methods for working with Arvados resources":{{site.baseurl}}/api/methods.html
API endpoint base: @https://{{ site.arvados_api_host }}/arvados/v1/users@
@@ -28,7 +28,7 @@ Side effects of creating a User.
h2. Resources
-Each User has, in addition to the usual "attributes of Arvados resources":/api/resources.html:
+Each User has, in addition to the usual "attributes of Arvados resources":{{site.baseurl}}/api/resources.html:
table(table table-bordered table-condensed).
|_. Attribute|_. Type|_. Description|_. Example|
diff --git a/doc/api/schema/VirtualMachine.html.textile.liquid b/doc/api/schema/VirtualMachine.html.textile.liquid
index f6dd561..6aa9c2b 100644
--- a/doc/api/schema/VirtualMachine.html.textile.liquid
+++ b/doc/api/schema/VirtualMachine.html.textile.liquid
@@ -12,7 +12,7 @@ A **VirtualMachine** represents...
h2. Methods
-See "REST methods for working with Arvados resources":/api/methods.html
+See "REST methods for working with Arvados resources":{{site.baseurl}}/api/methods.html
API endpoint base: @https://{{ site.arvados_api_host }}/arvados/v1/virtual_machines@
@@ -28,7 +28,7 @@ Side effects of creating a VirtualMachine.
h2. Resources
-Each VirtualMachine has, in addition to the usual "attributes of Arvados resources":/api/resources.html:
+Each VirtualMachine has, in addition to the usual "attributes of Arvados resources":{{site.baseurl}}/api/resources.html:
table(table table-bordered table-condensed).
|_. Attribute|_. Type|_. Description|_. Example|
diff --git a/doc/gen_api_schema_docs.py b/doc/gen_api_schema_docs.py
index 632a67f..239beda 100755
--- a/doc/gen_api_schema_docs.py
+++ b/doc/gen_api_schema_docs.py
@@ -33,7 +33,6 @@ layout: default
navsection: api
navmenu: Schema
title: {resource}
-navorder: {navorder}
---
h1. {resource}
@@ -42,7 +41,7 @@ A **{resource}** represents...
h2. Methods
-See "REST methods for working with Arvados resources":/api/methods.html
+ See "REST methods for working with Arvados resources":{{{{site.baseurl}}}}/api/methods.html
API endpoint base: @https://{{{{ site.arvados_api_host }}}}/arvados/v1/{res_api_endpoint}@
diff --git a/doc/index.html.liquid b/doc/index.html.liquid
index f9f51d6..4217a48 100644
--- a/doc/index.html.liquid
+++ b/doc/index.html.liquid
@@ -13,7 +13,7 @@ title: Arvados | Documentation
<p>manuals, guides, and references</p>
</div>
<div class="col-sm-6">
- <img src="images/dax.png" style="max-height: 10em"></img>
+ <img src="images/dax.png" style="max-height: 10em" alt="dax" />
</div>
</div>
</div>
diff --git a/doc/user/copying/agpl-3.0.html b/doc/user/copying/agpl-3.0.html
index 8b04e0a..aad493a 100644
--- a/doc/user/copying/agpl-3.0.html
+++ b/doc/user/copying/agpl-3.0.html
@@ -7,7 +7,7 @@ title: "GNU Affero General Public License"
<p style="text-align: center;">Version 3, 19 November 2007</p>
<p>Copyright © 2007 Free Software Foundation,
-Inc. <<a href="http://fsf.org/">http://fsf.org/</a>>
+Inc. <<a href="http://www.fsf.org/">http://fsf.org/</a>>
<br />
Everyone is permitted to copy and distribute verbatim copies
of this license document, but changing it is not allowed.</p>
commit 127f1e032068d83365d783e8fe8cad5f0117638a
Author: Peter Amstutz <peter.amstutz at curoverse.com>
Date: Thu Mar 20 15:01:25 2014 -0400
Added documentation for jobs and pipelines, and updated docs to reflect that "repository" has been split out from "script_version" and is now required.
diff --git a/doc/user/reference/job-and-pipeline-reference.html.textile.liquid b/doc/user/reference/job-and-pipeline-reference.html.textile.liquid
new file mode 100644
index 0000000..e9c24ec
--- /dev/null
+++ b/doc/user/reference/job-and-pipeline-reference.html.textile.liquid
@@ -0,0 +1,223 @@
+---
+layout: default
+navsection: userguide
+title: "Job and Pipeline Reference"
+...
+
+h2. Submitting jobs
+
+table(table table-bordered table-condensed).
+|_. Attribute |_. Type|_. Accepted values |_. Required|_. Description|
+|script |string |filename |yes |The actual script that will be run by crunch. Must be the name of an executable file in the crunch_scripts/ directory at the git revision specified by script_version.|
+|script_version |string |git branch, tag, or version hash |yes |The code version to run, which is available in the specified repository. May be a git hash or tag to specify an exact version, or a branch. If it is a branch, use the branch head.|
+|repository |string |name of git repository hosted by arvados |yes |The repository to search for script_version.|
+|script_parameters |object |any JSON object |yes |The input parameters for the job, with the parameter names as keys mapping to parameter values.|
+|minimum_script_version |string |git branch, tag, or version hash |no |The minimum acceptable script version when deciding whether to re-use a past job.|
+|exclude_script_versions|array of strings|git branch, tag, or version hash|no |Script versions to exclude when deciding whether to re-use a past job.|
+|nondeterministic |boolean | |no |If true, never re-use a past job, and flag this job so it will never be considered for re-use.|
+|no_reuse |boolean | |no |If true, do not re-use a past job, but this job may be re-used.|
+
+When a job is executed, the 'script_version' field is resolved to an exact git revision and the git hash for that revision is recorded in 'script_version'. If 'script_version' can't be resolved, the job submission will be rejected.
+
+h3. Reusing jobs
+
+Because Arvados records the exact version of the script, input parameters, and runtime environment [1] that was used to run the job, if the script is deterministic (meaning that the same code version is guaranteed to produce the same outputs from the same inputs) then it is possible to re-use the results of past jobs, and avoid re-running the computation to save time. Arvados uses the following algorithm to determine if a past job can be re-used:
+
+notextile. <div class="spaced-out">
+
+# If 'nondeterministic' or 'no_reuse' are true, always create a new job.
+# Find a list of acceptable values for 'script_version'. If 'minimum_script_version' is specified, this is the set of all revisions in the git commit graph between 'minimum_script_version' and 'script_version' (inclusive) [2]. If 'minimum_script_version' is not specified, only 'script_version' is added to the list. If 'exclude_script_versions' is specified, the listed versions are excluded from the list.
+# Select jobs have the same 'script' and 'script_parameters' attributes, and where the 'script_version' attribute is in the list of acceptable versions. Exclude failed jobs or where 'nondeterministic' is true.
+# If there is more than one candidate job, check that all selected past jobs actually did produce the same output.
+# If everything passed, re-use one of the selected past jobs (if there is more than one match, which job will be returned is undefined). Otherwise create a new job.
+
+fn1. As of this writing, versioning the runtime environment is still under development.
+
+fn2. This may include parallel branches if there is more than one path between 'minimum_script_version' and 'script_version' in the git commit graph. Use 'exclude_script_versions' to blacklist specific versions.
+
+</div>
+
+h3. Examples
+
+Run the script "crunch_scripts/hash.py" in the repository "you" using the "master" branch head. Arvados is allowed to re-use a previous job if the script_version of the past job is the same as the "master" branch head (i.e. there have not been any subsequent commits to "master").
+
+<pre>
+{
+ "script": "hash.py",
+ "repository": "you",
+ "script_version": "master",
+ "script_parameters": {
+ "input": "c1bad4b39ca5a924e481008009d94e32+210"
+ }
+}
+</pre>
+
+Run using exactly the version "d00220fb38d4b85ca8fc28a8151702a2b9d1dec5". Arvados is allowed to re-use a previous job if the script_version of that job is also "d00220fb38d4b85ca8fc28a8151702a2b9d1dec5".
+
+<pre>
+{
+ "script": "hash.py",
+ "repository": "you",
+ "script_version": "d00220fb38d4b85ca8fc28a8151702a2b9d1dec5",
+ "script_parameters": {
+ "input": "c1bad4b39ca5a924e481008009d94e32+210"
+ }
+}
+</pre>
+
+Arvados is allowed to re-use a previous job if the script_version of the past job is between "earlier_version_tag" and the head of the "master" branch (inclusive), but not "blacklisted_version_tag". If there are no previous jobs, run the job using the head of the "master" branch as specified in "script_version".
+
+<pre>
+{
+ "script": "hash.py",
+ "repository": "you",
+ "minimum_script_version": "earlier_version_tag",
+ "script_version": "master",
+ "exclude_script_versions", ["blacklisted_version_tag"],
+ "script_parameters": {
+ "input": "c1bad4b39ca5a924e481008009d94e32+210"
+ }
+}
+</pre>
+
+Run the script "crunch_scripts/monte-carlo.py" in the repository "you" using the "master" branch head. Because it is marked as "nondeterministic", never re-use previous jobs, and never re-use this job.
+
+<pre>
+{
+ "script": "monte-carlo.py",
+ "repository": "you",
+ "script_version": "master",
+ "nondeterministic": true,
+ "script_parameters": {
+ "input": "c1bad4b39ca5a924e481008009d94e32+210"
+ }
+}
+</pre>
+
+h2. Pipelines
+
+Pipelines consist of a set of "components". Each component is an Arvados job submission, so when a component job is submitted, Arvados may re-use past jobs based on the rules described above.
+
+table(table table-bordered table-condensed).
+|_. Attribute |_. Type |_. Accepted values |_. Required|_. Description|
+|name |string |any |yes |The human-readable name of the pipeline template.|
+|components |object |JSON object containing job submission objects|yes |The component jobs that make up the pipeline, with the component name as the key. |
+
+h3. Script parameters
+
+When used in a pipeline, each parameter in the 'script_parameters' attribute of a component job can specify that the input parameter must be supplied by the user, or the input parameter should be linked to the output of another component. To do this, the value of the parameter should be JSON object containing one of the following attributes:
+
+table(table table-bordered table-condensed).
+|_. Attribute |_. Type |_. Accepted values |_. Description|
+|default |any |any |The default value for this parameter.|
+|required |boolean |true or false |Specifies whether the parameter is required to have a value or not.|
+|dataclass |string |One of 'Collection', 'File' [3], 'number', or 'text' |Data type of this parameter.|
+|output_of |string |the name of another component in the pipeline |Specifies that the value of this parameter should be set to the 'output' attribute of the job that corresponds to the specified component.|
+
+The 'output_of' parameter is especially important, as this is how components are actually linked together to form a pipeline. Component jobs that depend on the output of other components do not run until the parent job completes and has produced output. If the parent job fails, the entire pipeline fails.
+
+fn3. The 'File' type refers to a specific file within a Keep collection in the form 'collection_hash/filename', for example '887cd41e9c613463eab2f0d885c6dd96+83/bob.txt'.
+
+h3. Examples
+
+This a pipeline named "Filter md5 hash values" with two components, "do_hash" and "filter". The "input" script parameter of the "do_hash" component is required to be filled in by the user, and the expected data type is "Collection". This also specifies that the "input" script parameter of the "filter" component is the output of "do_hash", so "filter" will not run until "do_hash" completes successfully. When the pipeline runs, past jobs that meet the criteria described above may be substituted for either or both components to avoid redundant computation.
+
+<pre>
+{
+ "name": "Filter md5 hash values",
+ "components": {
+ "do_hash": {
+ "script": "hash.py",
+ "repository": "you",
+ "script_version": "master",
+ "script_parameters": {
+ "input": {
+ "required": true,
+ "dataclass": "Collection"
+ }
+ },
+ },
+ "filter": {
+ "script": "0-filter.py",
+ "repository": "you",
+ "script_version": "master",
+ "script_parameters": {
+ "input": {
+ "output_of": "do_hash"
+ }
+ },
+ }
+ }
+}
+</pre>
+
+This pipeline consists of three components. The components "thing1" and "thing2" both depend on "cat_in_the_hat". Once the "cat_in_the_hat" job is complete, both "thing1" and "thing2" can run in parallel, because they do not depend on each other.
+
+<pre>
+{
+ "name": "Wreck the house",
+ "components": {
+ "cat_in_the_hat": {
+ "script": "cat.py",
+ "repository": "you",
+ "script_version": "master",
+ "script_parameters": { }
+ },
+ "thing1": {
+ "script": "thing1.py",
+ "repository": "you",
+ "script_version": "master",
+ "script_parameters": {
+ "input": {
+ "output_of": "cat_in_the_hat"
+ }
+ },
+ },
+ "thing2": {
+ "script": "thing2.py",
+ "repository": "you",
+ "script_version": "master",
+ "script_parameters": {
+ "input": {
+ "output_of": "cat_in_the_hat"
+ }
+ },
+ },
+ }
+}
+</pre>
+
+This pipeline consists of three components. The component "cleanup" depends on "thing1" and "thing2". Both "thing1" and "thing2" are started immediately and can run in parallel, because they do not depend on each other, but "cleanup" cannot begin until both "thing1" and "thing2" have completed.
+
+<pre>
+{
+ "name": "Clean the house",
+ "components": {
+ "thing1": {
+ "script": "thing1.py",
+ "repository": "you",
+ "script_version": "master",
+ "script_parameters": { }
+ },
+ "thing2": {
+ "script": "thing2.py",
+ "repository": "you",
+ "script_version": "master",
+ "script_parameters": { }
+ },
+ "cleanup": {
+ "script": "cleanup.py",
+ "repository": "you",
+ "script_version": "master",
+ "script_parameters": {
+ "mess1": {
+ "output_of": "thing1"
+ },
+ "mess2": {
+ "output_of": "thing2"
+ }
+ }
+ }
+ }
+}
+</pre>
diff --git a/doc/user/topics/keep.html.textile.liquid b/doc/user/topics/keep.html.textile.liquid
index dae133a..c4778cd 100644
--- a/doc/user/topics/keep.html.textile.liquid
+++ b/doc/user/topics/keep.html.textile.liquid
@@ -8,7 +8,7 @@ In Keep, information is stored in *data blocks*. Data blocks are normally betwe
In order to reassemble the file, Keep stores a *collection* data block which lists in sequence the data blocks that make up the original file. A collection data block may store the information for multiple files, including a directory structure.
-In this example we will use @c1bad4b39ca5a924e481008009d94e32+210@ which we added to Keep in "the first Keep tutorial":{{ site.baseurl }}/users/tutorial/tutorial-keep.html. First let us examine the contents of this collection using @arv keep get@:
+In this example we will use @c1bad4b39ca5a924e481008009d94e32+210@ which we added to Keep in "the first Keep tutorial":{{ site.baseurl }}/user/tutorials/tutorial-keep.html. First let us examine the contents of this collection using @arv keep get@:
<notextile>
<pre><code>~$ <span class="userinput">arv keep get c1bad4b39ca5a924e481008009d94e32+210</span>
diff --git a/doc/user/topics/running-pipeline-command-line.html.textile.liquid b/doc/user/topics/running-pipeline-command-line.html.textile.liquid
index 1b8550f..7940348 100644
--- a/doc/user/topics/running-pipeline-command-line.html.textile.liquid
+++ b/doc/user/topics/running-pipeline-command-line.html.textile.liquid
@@ -16,7 +16,8 @@ In "Writing a pipeline":{{ site.baseurl }}/user/tutorials/tutorial-firstscript.h
"script_parameters":{
"input": "887cd41e9c613463eab2f0d885c6dd96+83"
},
- "script_version":"<b>you</b>:master"
+ "repository":"<b>you</b>",
+ "script_version":"master"
},
"filter":{
"script":"0-filter.py",
@@ -25,7 +26,8 @@ In "Writing a pipeline":{{ site.baseurl }}/user/tutorials/tutorial-firstscript.h
"output_of":"do_hash"
}
},
- "script_version":"<b>you</b>:master"
+ "repository":"<b>you</b>",
+ "script_version":"master"
}
}
}
@@ -112,7 +114,6 @@ Now check the output:
<pre><code>~$ <span class="userinput">arv keep get 880b55fb4470b148a447ff38cacdd952+54/md5sum.txt</span>
44b8ae3fde7a8a88d2f7ebd237625b4f var-GS000016015-ASM.tsv.bz2
~$ <span class="userinput">arv keep get 490cd451c8108824b8a17e3723e1f236+19/0-filter.txt</span>
-~$
</code></pre>
</notextile>
diff --git a/doc/user/topics/tutorial-gatk-variantfiltration.html.textile.liquid b/doc/user/topics/tutorial-gatk-variantfiltration.html.textile.liquid
index f83c199..0248325 100644
--- a/doc/user/topics/tutorial-gatk-variantfiltration.html.textile.liquid
+++ b/doc/user/topics/tutorial-gatk-variantfiltration.html.textile.liquid
@@ -97,6 +97,7 @@ The Arvados distribution includes an example crunch script ("crunch_scripts/GATK
~$ <span class="userinput">cat >the_job <<EOF
{
"script":"GATK2-VariantFiltration",
+ "repository":"arvados",
"script_version":"$src_version",
"script_parameters":
{
diff --git a/doc/user/topics/tutorial-job1.html.textile.liquid b/doc/user/topics/tutorial-job1.html.textile.liquid
index 61eaa63..c100d6b 100644
--- a/doc/user/topics/tutorial-job1.html.textile.liquid
+++ b/doc/user/topics/tutorial-job1.html.textile.liquid
@@ -20,9 +20,9 @@ A request to run a crunch job are is described using a JSON object. For example
<pre><code>~$ <span class="userinput">cat >the_job <<EOF
{
"script": "hash",
- "script_version": "arvados:master",
- "script_parameters":
- {
+ "repository": "arvados",
+ "script_version": "master",
+ "script_parameters": {
"input": "c1bad4b39ca5a924e481008009d94e32+210"
}
}
@@ -34,7 +34,7 @@ EOF
* @<<EOF@ tells the shell to direct the following lines into the standard input for @cat@ up until it sees the line @EOF@
* @>the_job@ redirects standard output to a file called @the_job@
* @"script"@ specifies the name of the script to run. The script is searched for in the "crunch_scripts/" subdirectory of the @git@ checkout specified by @"script_version"@.
-* @"script_version"@ specifies the version of the script that you wish to run. This can be in the form of an explicit @git@ revision hash, or in the form "repository:branch" (in which case it will take the HEAD of the specified branch). Arvados logs the script version that was used in the run, enabling you to go back and re-run any past job with the guarantee that the exact same code will be used as was used in the previous run. You can access a list of available @git@ repositories on the Arvados workbench under "Compute %(rarr)→% Code repositories":http://{{site.arvados_workbench_host}}/repositories .
+* @"script_version"@ specifies the version of the script that you wish to run. This can be in the form of an explicit @git@ revision hash, or in the form "repository:branch" (in which case it will take the HEAD of the specified branch). Arvados logs the script version that was used in the run, enabling you to go back and re-run any past job with the guarantee that the exact same code will be used as was used in the previous run. You can access a list of available @git@ repositories on the Arvados workbench under "Compute %(rarr)→% Code repositories":https://{{site.arvados_workbench_host}}/repositories .
* @"script_parameters"@ are provided to the script. In this case, the input is the locator for the collection that we inspected in the previous section.
Use @arv job create@ to actually submit the job. It should print out a JSON object which describes the newly created job:
@@ -86,7 +86,7 @@ The job is now queued and will start running as soon as it reaches the front of
h2. Monitor job progress
-Go to the "Workbench dashboard":http://{{site.arvados_workbench_host}}. Your job should be at the top of the "Recent jobs" table. This table refreshes automatically. When the job has completed successfully, it will show <span class="label label-success">finished</span> in the *Status* column.
+Go to the "Workbench dashboard":https://{{site.arvados_workbench_host}}. Your job should be at the top of the "Recent jobs" table. This table refreshes automatically. When the job has completed successfully, it will show <span class="label label-success">finished</span> in the *Status* column.
On the command line, you can access log messages while the job runs using @arv job log_tail_follow@:
@@ -96,7 +96,7 @@ This will print out the last several lines of the log for that job.
h2. Inspect the job output
-On the "Workbench dashboard":http://{{site.arvados_workbench_host}}, look for the *Output* column of the *Recent jobs* table. Click on the link under *Output* for your job to go to the files page with the job output. The files page lists all the files that were output by the job. Click on the link under the *files* column to view a file, or click on the download icon <span class="glyphicon glyphicon-download-alt"></span> to download the output file.
+On the "Workbench dashboard":https://{{site.arvados_workbench_host}}, look for the *Output* column of the *Recent jobs* table. Click on the link under *Output* for your job to go to the files page with the job output. The files page lists all the files that were output by the job. Click on the link under the *files* column to view a file, or click on the download icon <span class="glyphicon glyphicon-download-alt"></span> to download the output file.
On the command line, you can use @arv job get@ to access a JSON object describing the output:
diff --git a/doc/user/topics/tutorial-parallel.html.textile.liquid b/doc/user/topics/tutorial-parallel.html.textile.liquid
index 9d08b69..6dbdb8a 100644
--- a/doc/user/topics/tutorial-parallel.html.textile.liquid
+++ b/doc/user/topics/tutorial-parallel.html.textile.liquid
@@ -40,7 +40,8 @@ You should now be able to run your new script using Crunch, with "script" referr
<pre><code>~/<b>you</b>/crunch_scripts$ <span class="userinput">cat >~/the_job <<EOF
{
"script": "parallel-hash.py",
- "script_version": "<b>you</b>:master",
+ "repository": "<b>you</b>",
+ "script_version": "master",
"script_parameters":
{
"input": "887cd41e9c613463eab2f0d885c6dd96+83"
diff --git a/doc/user/tutorials/running-external-program.html.textile.liquid b/doc/user/tutorials/running-external-program.html.textile.liquid
index b555d77..758faa5 100644
--- a/doc/user/tutorials/running-external-program.html.textile.liquid
+++ b/doc/user/tutorials/running-external-program.html.textile.liquid
@@ -53,7 +53,8 @@ You should now be able to run your new script using Crunch, with "script" referr
"dataclass": "Collection"
}
},
- "script_version":"<b>you</b>:master"
+ "repository":"<b>you</b>",
+ "script_version":"master"
}
}
}
@@ -62,4 +63,4 @@ EOF
</code></pre>
</notextile>
-Your new pipeline template will appear on the "Workbench %(rarr)→% Compute %(rarr)→% Pipeline templates":http://{{ site.arvados_workbench_host }}/pipeline_instances page. You can run the "pipeline using workbench":tutorial-pipeline-workbench.html
+Your new pipeline template will appear on the "Workbench %(rarr)→% Compute %(rarr)→% Pipeline templates":https://{{ site.arvados_workbench_host }}/pipeline_instances page. You can run the "pipeline using workbench":tutorial-pipeline-workbench.html
diff --git a/doc/user/tutorials/tutorial-firstscript.html.textile.liquid b/doc/user/tutorials/tutorial-firstscript.html.textile.liquid
index 245e890..a3b7e54 100644
--- a/doc/user/tutorials/tutorial-firstscript.html.textile.liquid
+++ b/doc/user/tutorials/tutorial-firstscript.html.textile.liquid
@@ -22,7 +22,7 @@ First, you should do some basic configuration for git (you only need to do this
~$ <span class="userinput">git config --global user.email <b>you</b>@example.com</span></code></pre>
</notextile>
-On the Arvados Workbench, navigate to "Compute %(rarr)→% Code repositories":http://{{site.arvados_workbench_host}}/repositories . You should see a repository with your user name listed in the *name* column. Next to *name* is the column *push_url*. Copy the *push_url* value associated with your repository. This should look like <notextile><code>git at git.{{ site.arvados_api_host }}:<b>you</b>.git</code></notextile>.
+On the Arvados Workbench, navigate to "Compute %(rarr)→% Code repositories":https://{{site.arvados_workbench_host}}/repositories . You should see a repository with your user name listed in the *name* column. Next to *name* is the column *push_url*. Copy the *push_url* value associated with your repository. This should look like <notextile><code>git at git.{{ site.arvados_api_host }}:<b>you</b>.git</code></notextile>.
Next, on the Arvados virtual machine, clone your git repository:
@@ -111,7 +111,8 @@ Next, create a file that contains the pipeline definition:
"dataclass": "Collection"
}
},
- "script_version":"<b>you</b>:master"
+ "repository":"<b>you</b>",
+ "script_version":"master"
}
}
}
@@ -126,7 +127,8 @@ EOF
* @"components"@ is a set of scripts that make up the pipeline
* The component is listed with a human-readable name (@"do_hash"@ in this example)
* @"script"@ specifies the name of the script to run. The script is searched for in the "crunch_scripts/" subdirectory of the @git@ checkout specified by @"script_version"@.
-* @"script_version"@ specifies the version of the script that you wish to run. This can be in the form of an explicit @git@ revision hash, or in the form "repository:branch" (in which case it will take the HEAD of the specified branch). Arvados logs the script version that was used in the run, enabling you to go back and re-run any past job with the guarantee that the exact same code will be used as was used in the previous run. You can access a list of available @git@ repositories on the Arvados workbench under "Compute %(rarr)→% Code repositories":http://{{site.arvados_workbench_host}}//repositories .
+* @"repository"@ is the git repository to search for the script version. You can access a list of available @git@ repositories on the Arvados workbench under "Compute %(rarr)→% Code repositories":https://{{site.arvados_workbench_host}}//repositories .
+* @"script_version"@ specifies the version of the script that you wish to run. This can be in the form of an explicit @git@ revision hash, a tag, or a branch (in which case it will take the HEAD of the specified branch). Arvados logs the script version that was used in the run, enabling you to go back and re-run any past job with the guarantee that the exact same code will be used as was used in the previous run.
* @"script_parameters"@ describes the parameters for the script. In this example, there is one parameter called @input@ which is @required@ and is a @Collection at .
Now, use @arv pipeline_template create@ tell Arvados about your pipeline template:
@@ -136,4 +138,4 @@ Now, use @arv pipeline_template create@ tell Arvados about your pipeline templat
</code></pre>
</notextile>
-Your new pipeline template will appear on the "Workbench %(rarr)→% Compute %(rarr)→% Pipeline templates":http://{{ site.arvados_workbench_host }}/pipeline_instances page. You can run the "pipeline using workbench":tutorial-pipeline-workbench.html
+Your new pipeline template will appear on the "Workbench %(rarr)→% Compute %(rarr)→% Pipeline templates":https://{{ site.arvados_workbench_host }}/pipeline_instances page. You can run the "pipeline using workbench":tutorial-pipeline-workbench.html
diff --git a/doc/user/tutorials/tutorial-new-pipeline.html.textile.liquid b/doc/user/tutorials/tutorial-new-pipeline.html.textile.liquid
index b09e624..a4bad58 100644
--- a/doc/user/tutorials/tutorial-new-pipeline.html.textile.liquid
+++ b/doc/user/tutorials/tutorial-new-pipeline.html.textile.liquid
@@ -43,7 +43,8 @@ Next, create a file that contains the pipeline definition:
"dataclass": "Collection"
}
},
- "script_version":"<b>you</b>:master"
+ "repository":"<b>you</b>",
+ "script_version":"master"
},
"filter":{
"script":"0-filter.py",
@@ -52,7 +53,8 @@ Next, create a file that contains the pipeline definition:
"output_of":"do_hash"
}
},
- "script_version":"<b>you</b>:master"
+ "repository":"<b>you</b>",
+ "script_version":"master"
}
}
}
@@ -69,5 +71,5 @@ Now, use @arv pipeline_template create@ tell Arvados about your pipeline templat
</code></pre>
</notextile>
-Your new pipeline template will appear on the "Workbench %(rarr)→% Compute %(rarr)→% Pipeline templates":http://{{ site.arvados_workbench_host }}/pipeline_instances page.
+Your new pipeline template will appear on the "Workbench %(rarr)→% Compute %(rarr)→% Pipeline templates":https://{{ site.arvados_workbench_host }}/pipeline_instances page.
diff --git a/doc/user/tutorials/tutorial-pipeline-workbench.html.textile.liquid b/doc/user/tutorials/tutorial-pipeline-workbench.html.textile.liquid
index 52dafb7..46aadd3 100644
--- a/doc/user/tutorials/tutorial-pipeline-workbench.html.textile.liquid
+++ b/doc/user/tutorials/tutorial-pipeline-workbench.html.textile.liquid
@@ -6,11 +6,11 @@ title: "Running a pipeline using Workbench"
notextile. <div class="spaced-out">
-# Go to "Collections":http://{{ site.arvados_workbench_host }}/collections .
+# Go to "Collections":https://{{ site.arvados_workbench_host }}/collections .
# On the collections page, go to the search box <span class="glyphicon glyphicon-search"></span> and search for "tutorial".
# This should yield a collection with the contents "var-GS000016015-ASM.tsv.bz2"
# Click on the check box to the left of "var-GS000016015-ASM.tsv.bz2". This puts the collection in your persistent selection list. Click on the paperclip <span class="glyphicon glyphicon-paperclip"></span> in the upper right to get a dropdown menu listing your current selections.
-# Go to "Pipeline templates":http://{{ site.arvados_workbench_host }}/pipeline_templates .
+# Go to "Pipeline templates":https://{{ site.arvados_workbench_host }}/pipeline_templates .
# Look for a pipeline named "Tutorial pipeline".
# Click on the play button <span class="glyphicon glyphicon-play"></span> to the left of "Tutorial pipeline". This will take you to a new page to configure the pipeline.
# Under *parameter* look for "input". Set the value of "input" by clicking on on "none" to get a editing popup. At the top of the selection list in the editing popup will be the collection that you selected in step 4.
-----------------------------------------------------------------------
hooks/post-receive
--
More information about the arvados-commits
mailing list