10499: Warn about user guide sections that rely on crunch1.

diff --git a/doc/_includes/_crunch1only_begin.liquid b/doc/_includes/_crunch1only_begin.liquid
new file mode 100644 (file)
index 0000000..5c08d1e
--- /dev/null
+++ b/doc/_includes/_crunch1only_begin.liquid
@@ -0,0 +1,2 @@
+{% include 'notebox_begin_warning' %}
+This section assumes the legacy Jobs API is available. Some newer installations have already disabled the Jobs API in favor of the Containers API.

diff --git a/doc/_includes/_crunch1only_end.liquid b/doc/_includes/_crunch1only_end.liquid
new file mode 100644 (file)
index 0000000..f8b437a
--- /dev/null
+++ b/doc/_includes/_crunch1only_end.liquid
@@ -0,0 +1 @@
+{% include 'notebox_end' %}

diff --git a/doc/_includes/_notebox_begin_warning.liquid b/doc/_includes/_notebox_begin_warning.liquid
new file mode 100644 (file)
index 0000000..9f97e74
--- /dev/null
+++ b/doc/_includes/_notebox_begin_warning.liquid
@@ -0,0 +1,2 @@
+<div class="alert alert-block alert-warning">
+  <h4>Note:</h4>

diff --git a/doc/_includes/_pipeline_deprecation_notice.liquid b/doc/_includes/_pipeline_deprecation_notice.liquid
index 682511f70c37ac9f2d31960adc8a3d07a712efd5..a2747b0a5916b76c34df8466a9a08069676feb3c 100644 (file)
--- a/doc/_includes/_pipeline_deprecation_notice.liquid
+++ b/doc/_includes/_pipeline_deprecation_notice.liquid
@@ -1,3 +1,3 @@
-{% include 'notebox_begin' %}
+{% include 'notebox_begin_warning' %}
 Arvados pipeline templates are deprecated.  The recommended way to develop new workflows for Arvados is using the "Common Workflow Language":{{site.baseurl}}/user/cwl/cwl-runner.html.
 {% include 'notebox_end' %}

diff --git a/doc/user/topics/arv-run.html.textile.liquid b/doc/user/topics/arv-run.html.textile.liquid
index 8d1aca63057f44f22abb5811c2ef73c8478e4129..93fc2c0f34e4a3da4388560b265d7c189da30fa3 100644 (file)
--- a/doc/user/topics/arv-run.html.textile.liquid
+++ b/doc/user/topics/arv-run.html.textile.liquid
@@ -4,6 +4,10 @@ navsection: userguide
 title: "Using arv-run"
 ...
 
+{% include 'crunch1only_begin' %}
+On those sites, the features described here are not yet implemented.
+{% include 'crunch1only_end' %}
+
 The @arv-run@ command enables you create Arvados pipelines at the command line that fan out to multiple concurrent tasks across Arvados compute nodes.
 
 {% include 'tutorial_expectations' %}

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 9a2e12c09677beb59495b95404caea2c8622be5a..14c88d1311194b1b576f94209a6dcbf56469d494 100644 (file)
--- a/doc/user/topics/running-pipeline-command-line.html.textile.liquid
+++ b/doc/user/topics/running-pipeline-command-line.html.textile.liquid
@@ -4,6 +4,10 @@ navsection: userguide
 title: "Running an Arvados pipeline"
 ...
 
+{% include 'crunch1only_begin' %}
+If the Jobs API is not available, use the "Common Workflow Language":{{site.baseurl}}/user/cwl/cwl-runner.html instead.
+{% include 'crunch1only_end' %}
+
 This tutorial demonstrates how to use the command line to run the same pipeline as described in "running a pipeline using Workbench.":{{site.baseurl}}/user/tutorials/tutorial-pipeline-workbench.html
 
 {% include 'tutorial_expectations' %}

diff --git a/doc/user/tutorials/tutorial-pipeline-workbench.html.textile.liquid b/doc/user/tutorials/tutorial-pipeline-workbench.html.textile.liquid
index fac573aca9bdbc30a1f93b8f75e4af10e0818cfe..6537fda0d85be61ca82892e00367a7df7f97f20d 100644 (file)
--- a/doc/user/tutorials/tutorial-pipeline-workbench.html.textile.liquid
+++ b/doc/user/tutorials/tutorial-pipeline-workbench.html.textile.liquid
@@ -4,6 +4,10 @@ navsection: userguide
 title: "Running a pipeline using Workbench"
 ...
 
+{% include 'crunch1only_begin' %}
+On those sites, the details will be slightly different and the example pipeline might not be available.
+{% include 'crunch1only_end' %}
+
 A "pipeline" (sometimes called a "workflow" in other systems) is a sequence of steps that apply various programs or tools to transform input data to output data.  Pipelines are the principal means of performing computation with Arvados.  This tutorial demonstrates how to run a single-stage pipeline to take a small data set of paired-end reads from a sample "exome":https://en.wikipedia.org/wiki/Exome in "FASTQ":https://en.wikipedia.org/wiki/FASTQ_format format and align them to "Chromosome 19":https://en.wikipedia.org/wiki/Chromosome_19_%28human%29 using the "bwa mem":http://bio-bwa.sourceforge.net/ tool, producing a "Sequence Alignment/Map (SAM)":https://samtools.github.io/ file.  This tutorial will introduce the following Arvados features:
 
 <div>