[arvados.git] / doc / user / tutorials / running-external-program.html.textile.liquid

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layout: default
navsection: userguide
title: "Writing a pipeline template"
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This tutorial demonstrates how to construct a two stage pipeline template that uses the "bwa mem":http://bio-bwa.sourceforge.net/ tool to produce a "Sequence Alignment/Map (SAM)":https://samtools.github.io/ file, then uses the "Picard SortSam tool":http://picard.sourceforge.net/command-line-overview.shtml#SortSam to produce a BAM (Binary Alignment/Map) file.

{% include 'tutorial_expectations' %}

Use the following command to create an empty template using @arv create pipeline_template@:

<notextile>
<pre><code>~$ <span class="userinput">arv create pipeline_template</span></code></pre>
</notextile>

This will open the template record in an interactive text editor (as specified by $EDITOR or $VISUAL, otherwise defaults to @nano@).  Now, update the contents of the editor with the following content:

<notextile>{% code 'tutorial_bwa_sortsam_pipeline' as javascript %}</notextile>

* @"name"@ is a human-readable name for the pipeline.
* @"components"@ is a set of scripts or commands that make up the pipeline.  Each component is given an identifier (@"bwa-mem"@ and @"SortSam"@) in this example).
** Each entry in components @"components"@ is an Arvados job submission.  For more information about individual jobs, see the "job object reference":{{site.baseurl}}/api/schema/Job.html and "job create method.":{{site.baseurl}}/api/methods/jobs.html#create
* @"repository"@, @"script_version"@, and @"script"@ indicate that we intend to use the external @"run-command"@ tool wrapper that is part of the Arvados.  These parameters are described in more detail in "Writing a script":tutorial-firstscript.html.
* @"runtime_constraints"@ describes runtime resource requirements for the component.
** @"docker_image"@ specifies the "Docker":https://www.docker.com/ runtime environment in which to run the job.  The Docker image @"bcosc/arv-base-java"@ supplied here has the Java runtime environment, bwa, and samtools installed.
** @"arvados_sdk_version"@ specifies a version of the Arvados SDK to load alongside the job's script. The example uses 'master'. If you would like to use a specific version of the sdk, you can find it in the "Arvados Python sdk repository":https://arvados.org/projects/arvados/repository/revisions/master/show/sdk/python under *Latest revisions*.
* @"script_parameters"@ describes the component parameters.
** @"command"@ is the actual command line to invoke the @bwa@ and then @SortSam@.  The notation @$()@ denotes macro substitution commands evaluated by the run-command tool wrapper.
** @"task.stdout"@ indicates that the output of this command should be captured to a file.
** @$(node.cores)@ evaluates to the number of cores available on the compute node at time the command is run.
** @$(tmpdir)@ evaluates to the local path for temporary directory the command should use for scratch data.
** @$(reference_collection)@ evaluates to the script_parameter @"reference_collection"@
** @$(dir $(...))@ constructs a local path to a directory representing the supplied Arvados collection.
** @$(file $(...))@ constructs a local path to a given file within the supplied Arvados collection.
** @$(glob $(...))@ searches the specified path based on a file glob pattern and evalutes to the first result.
** @$(basename $(...))@ evaluates to the supplied path with leading path portion and trailing filename extensions stripped
* @"output_of"@ indicates that the @output@ of the @bwa-mem@ component should be used as the @"input"@ script parameter of @SortSam@.  Arvados uses these dependencies between components to automatically determine the correct order to run them.

When using @run-command@, the tool should write its output to the current working directory.  The output will be automatically uploaded to Keep when the job completes.

See the "run-command reference":{{site.baseurl}}/user/topics/run-command.html for more information about using @run-command@.

h2. Running your pipeline

Your new pipeline template should appear at the top of the Workbench "pipeline&nbsp;templates":{{site.arvados_workbench_host}}/pipeline_templates page.  You can run your pipeline "using Workbench":tutorial-pipeline-workbench.html or the "command line.":{{site.baseurl}}/user/topics/running-pipeline-command-line.html

Test data is available in the "Arvados Tutorial":{{site.arvados_workbench_host}}/projects/qr1hi-j7d0g-u7zg1qdaowykd8d project:

* Choose <i class="fa fa-fw fa-archive"></i> "Tutorial chromosome 19 reference (2463fa9efeb75e099685528b3b9071e0+438)":{{site.arvados_workbench_host}}/collections/2463fa9efeb75e099685528b3b9071e0+438 for the "reference_collection" parameter
* Choose <i class="fa fa-fw fa-archive"></i> "Tutorial sample exome (3229739b505d2b878b62aed09895a55a+142)":{{site.arvados_workbench_host}}/collections/3229739b505d2b878b62aed09895a55a+142 for the "sample" parameter

For more information and examples for writing pipelines, see the "pipeline template reference":{{site.baseurl}}/api/schema/PipelineTemplate.html

h2. Re-using your pipeline run

Arvados allows users to re-use jobs that have the same inputs in order to save computing time and resources. Users are able to change a job downstream without re-computing earlier jobs. This section shows what parameters you need to version control in order to make sure Arvados will not re-compute your jobs. 

Note: Job reuse can only happen if all input collections do not change.

* @"arvados_sdk_version"@ : The arvados_sdk_version parameter is used to download the specific version of the Arvados sdk into the docker image. The latest version can be found in the "Arvados Python sdk repository":https://arvados.org/projects/arvados/repository/revisions/master/show/sdk/python under *Latest revisions*.
* @"script_version"@ : The script_version is the commit hash of the git branch that the crunch script resides. This information can be found in your git repository by using the following command:

<notextile>
<pre><code>~$ <span class="userinput">git rev-parse HEAD</span></code></pre>
</notextile>

* @"docker_image"@ : This specifies the "Docker":https://www.docker.com/ runtime environment where job's run their scripts. Docker version control is similar to git, you can commit and push changes to your images. In order to version control your docker image on arvados, you must use the docker image hash which is found on the "Collection page":https://cloud.curoverse.com/collections/qr1hi-4zz18-dov6im679g3jr1n as the *Content address*.