[ARVADOS] created: 42f433ac4486c18fa6408d5f942dc394e5ff149e

[Git user]

        at  42f433ac4486c18fa6408d5f942dc394e5ff149e (commit)


commit 42f433ac4486c18fa6408d5f942dc394e5ff149e
Author: Tom Clegg <tom at curoverse.com>
Date:   Fri Nov 11 10:42:21 2016 -0500

    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
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
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
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 682511f..a2747b0 100644
--- 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 8d1aca6..93fc2c0 100644
--- 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 9a2e12c..14c88d1 100644
--- 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 fac573a..6537fda 100644
--- 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>

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