---
layout: default
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-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)":{{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-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

2014-07-25 18:05:36 +0000 -- pipeline_instance qr1hi-d1hrv-d14trje19pna7f2
bwa-mem qr1hi-8i9sb-67n1qvsronmd2z6 {:done=>0, :running=>1, :failed=>0, :todo=>0}

2014-07-25 18:05:46 +0000 -- pipeline_instance qr1hi-d1hrv-d14trje19pna7f2
bwa-mem qr1hi-8i9sb-67n1qvsronmd2z6 49bae1066f4ebce72e2587a3efa61c7d+88
</code></pre>
</notextile>

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.

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.