---
layout: default
navsection: userguide
-title: "Running a pipeline on the command line"
+title: "Running an Arvados pipeline"
...
+{% comment %}
+Copyright (C) The Arvados Authors. All rights reserved.
-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
+SPDX-License-Identifier: CC-BY-SA-3.0
+{% endcomment %}
+
+{% 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-workflow-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:
-* <i class="fa fa-fw fa-gear"></i> "Tutorial align using bwa mem (qr1hi-p5p6p-itzkwxblfermlwv)":https://{{ site.arvados_workbench_host }}/pipeline_templates/qr1hi-p5p6p-itzkwxblfermlwv
-* <i class="fa fa-fw fa-archive"></i> "Tutorial chromosome 19 reference (2463fa9efeb75e099685528b3b9071e0+438)":https://{{ site.arvados_workbench_host }}/collections/2463fa9efeb75e099685528b3b9071e0+438
-* <i class="fa fa-fw fa-archive"></i> "Tutorial sample exome (3229739b505d2b878b62aed09895a55a+142)":https://{{ site.arvados_workbench_host }}/collections/3229739b505d2b878b62aed09895a55a+142
+* <i class="fa fa-fw fa-gear"></i> "Tutorial align using bwa mem (qr1hi-p5p6p-itzkwxblfermlwv)":{{site.arvados_workbench_host}}/pipeline_templates/qr1hi-p5p6p-itzkwxblfermlwv
+* <i class="fa fa-fw fa-archive"></i> "Tutorial chromosome 19 reference (2463fa9efeb75e099685528b3b9071e0+438)":{{site.arvados_workbench_host}}/collections/2463fa9efeb75e099685528b3b9071e0+438
+* <i class="fa fa-fw fa-archive"></i> "Tutorial sample exome (3229739b505d2b878b62aed09895a55a+142)":{{site.arvados_workbench_host}}/collections/3229739b505d2b878b62aed09895a55a+142
Use @arv pipeline run@ to run the pipeline, supplying the inputs to the bwa-mem component on the command line:
<notextile>
-<pre><code>~$ <span class="userinput">arv pipeline run --run-here --template qr1hi-p5p6p-itzkwxblfermlwv bwa-mem::reference_collection=2463fa9efeb75e099685528b3b9071e0+438 bwa-mem::sample=3229739b505d2b878b62aed09895a55a+142</span>
+<pre><code>~$ <span class="userinput">arv pipeline run --run-pipeline-here --template qr1hi-p5p6p-itzkwxblfermlwv bwa-mem::reference_collection=2463fa9efeb75e099685528b3b9071e0+438 bwa-mem::sample=3229739b505d2b878b62aed09895a55a+142</span>
2014-07-25 18:05:26 +0000 -- pipeline_instance qr1hi-d1hrv-d14trje19pna7f2
bwa-mem qr1hi-8i9sb-67n1qvsronmd2z6 queued 2014-07-25T18:05:25Z
</code></pre>
</notextile>
-This instantiates your pipeline and displays a live feed of its status. 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.
+
-Arvados adds each pipeline component to the job queue as its dependencies are satisfied (or immediately if it has no dependencies) and finishes when all components are completed or failed and there is no more work left to do.
+@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 status feed 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>
29226 ./HWI-ST1027_129_D0THKACXX.1_1.sam
</code></pre>
</notextile>
+
+h2. Re-using existing jobs and outputs
+
+When satisfying a pipeline component that is not marked as nondeterministic in the pipeline template, @arv pipeline run@ checks for a previously submitted job that satisfies the component's requirements. If such a job is found, @arv pipeline run@ uses the existing job rather than submitting a new one. Usually this is a safe way to conserve time and compute resources. In some cases it's desirable to re-run jobs with identical specifications (e.g., to demonstrate that a job or entire pipeline thought to be repeatable is in fact repeatable). For such cases, job re-use features can be disabled entirely by passing the @--no-reuse@ flag to the @arv pipeline run@ command.
projects / arvados.git / blobdiff