Merge branch 'master' into 10215-arvados-cwl-runner-version

[arvados.git] / doc / user / topics / running-pipeline-command-line.html.textile.liquid

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 8c8dd149b7c71bdf2d5ff3d4f49b29431191611b..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
@@ -1,12 +1,17 @@
 ---
 layout: default
 navsection: userguide
 ---
 layout: default
 navsection: userguide

-title: "Running a pipeline on the command line"
+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' %}
 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' %}

+{% include 'tutorial_cluster_name' %}

 
 When you use the command line, you must use Arvados unique identifiers to refer to objects.  The identifiers in this example correspond to the following Arvados objects:
 
 
 When you use the command line, you must use Arvados unique identifiers to refer to objects.  The identifiers in this example correspond to the following Arvados objects:
 


@@ -32,9 +37,10 @@ bwa-mem qr1hi-8i9sb-67n1qvsronmd2z6 49bae1066f4ebce72e2587a3efa61c7d+88
 
 This instantiates your pipeline and displays periodic status reports in your terminal window. The new pipeline instance will also show up on the Workbench Dashboard.
 
 
 This instantiates your pipeline and displays periodic status reports in your terminal window. The new pipeline instance will also show up on the Workbench Dashboard.
 

+

 @arv pipeline run@ submits a job for each pipeline component as soon as the component's inputs are known (i.e., any dependencies are satsified). It terminates when there is no work left to do: this means either all components are satisfied and all jobs have completed successfully, _or_ one or more jobs have failed and it is therefore unproductive to submit any further jobs.
 
 @arv pipeline run@ submits a job for each pipeline component as soon as the component's inputs are known (i.e., any dependencies are satsified). It terminates when there is no work left to do: this means either all components are satisfied and all jobs have completed successfully, _or_ one or more jobs have failed and it is therefore unproductive to submit any further jobs.
 

-The Keep locators of the output of of the @bwa-mem@ components are available from the last status report shown above:
+The Keep locators of the output of the @bwa-mem@ components are available from the last status report shown above:

 
 <notextile>
 <pre><code>~$ <span class="userinput">arv keep ls -s 49bae1066f4ebce72e2587a3efa61c7d+88</span>
 
 <notextile>
 <pre><code>~$ <span class="userinput">arv keep ls -s 49bae1066f4ebce72e2587a3efa61c7d+88</span>