10576: Tweak Docker docs and add pipeline deprecation notice.

diff --git a/doc/_config.yml b/doc/_config.yml
index 97f45db56beebf9aebe331fd50c3e9e992f2bebb..c2891d7cff1b4f20701839186e7a5deced1f3245 100644 (file)
--- a/doc/_config.yml
+++ b/doc/_config.yml
@@ -56,12 +56,12 @@ navbar:
       - user/tutorials/writing-cwl-workflow.html.textile.liquid
       - user/cwl/cwl-style.html.textile.liquid
       - user/cwl/cwl-extensions.html.textile.liquid
+      - user/topics/arv-docker.html.textile.liquid
       - user/tutorials/running-external-program.html.textile.liquid
       - user/topics/crunch-tools-overview.html.textile.liquid
       - user/tutorials/tutorial-firstscript.html.textile.liquid
       - user/tutorials/tutorial-submit-job.html.textile.liquid
       - user/topics/tutorial-parallel.html.textile.liquid
-      - user/topics/arv-docker.html.textile.liquid
     - Develop a web service:
       - user/topics/arv-web.html.textile.liquid
     - Reference:

diff --git a/doc/user/examples/crunch-examples.html.textile.liquid b/doc/user/examples/crunch-examples.html.textile.liquid
index 21f30cc61d3b6d1d6572f97c7d67068c342b0e66..d1c7f12c8848663ba6d900fe600a924d022e6e53 100644 (file)
--- a/doc/user/examples/crunch-examples.html.textile.liquid
+++ b/doc/user/examples/crunch-examples.html.textile.liquid
@@ -4,6 +4,8 @@ navsection: userguide
 title: "Scripts provided by Arvados"
 ...
 
+{% include 'pipeline_deprecation_notice' %}
+
 Several crunch scripts are included with Arvados in the "/crunch_scripts directory":https://dev.arvados.org/projects/arvados/repository/revisions/master/show/crunch_scripts. They are intended to provide examples and starting points for writing your own scripts.
 
 h4. bwa-aln

diff --git a/doc/user/reference/job-pipeline-ref.html.textile.liquid b/doc/user/reference/job-pipeline-ref.html.textile.liquid
index 643e6bb3df4ffa5db2a8d388b7c8b1412502cafa..9e8b2cf34b22621f0c3185f7cdcd7a66a182fe54 100644 (file)
--- a/doc/user/reference/job-pipeline-ref.html.textile.liquid
+++ b/doc/user/reference/job-pipeline-ref.html.textile.liquid
@@ -4,4 +4,6 @@ navsection: userguide
 title: "Pipeline template reference"
 ...
 
+{% include 'pipeline_deprecation_notice' %}
+
 Pipeline template options are described on the "pipeline template schema page.":{{site.baseurl}}/api/methods/pipeline_templates.html

diff --git a/doc/user/topics/arv-docker.html.textile.liquid b/doc/user/topics/arv-docker.html.textile.liquid
index 1a31d126da698495eca853b72e1dcca9424c94a1..5ccd5ac476bdc8e3cda0cb4891869ee68e6cf2d8 100644 (file)
--- a/doc/user/topics/arv-docker.html.textile.liquid
+++ b/doc/user/topics/arv-docker.html.textile.liquid
@@ -184,13 +184,13 @@ arvados/jobs-with-r             latest      33ea6b877923  qr1hi-4zz18-3fk2px2ji2
 </code></pre>
 </notextile>
 
-You are now able to specify the runtime environment for your program using the @docker_image@ field of the @runtime_constaints@ section of your pipeline components:
+You are now able to specify the runtime environment for your program using @DockerRequirement@ in your workflow:
 
-<notextile>
-{% code 'example_docker' as javascript %}
-</notextile>
-
-* The @docker_image@ field can be one of: the Docker repository name (as shown above), the Docker image hash, or the Arvados collection portable data hash.
+<pre>
+hints:
+  DockerRequirement:
+    dockerPull: arvados/jobs-with-r
+</pre>
 
 h2. Share Docker images
 

diff --git a/doc/user/topics/run-command.html.textile.liquid b/doc/user/topics/run-command.html.textile.liquid
index 78839196967260dace26bc7791c72656ab85d0c1..ac40458e3f73d43a7978013faa5597d5c8f7a667 100644 (file)
--- a/doc/user/topics/run-command.html.textile.liquid
+++ b/doc/user/topics/run-command.html.textile.liquid
@@ -4,6 +4,8 @@ navsection: userguide
 title: "run-command reference"
 ...
 
+{% include 'pipeline_deprecation_notice' %}
+
 The @run-command@ crunch script enables you run command line programs.
 
 {% include 'tutorial_expectations_workstation' %}