---
layout: default
navsection: userguide
-title: "Using Crunch to run external programs"
+title: "Writing a pipeline template"
...
-This tutorial demonstrates how to use Crunch to run an external program by writting a wrapper using the Python SDK.
+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.
-*This tutorial assumes that you are "logged into an Arvados VM instance":{{site.baseurl}}/user/getting_started/ssh-access.html#login, and have a "working environment.":{{site.baseurl}}/user/getting_started/check-environment.html*
+{% include 'tutorial_expectations' %}
-In this tutorial, you will use the external program @md5sum@ to compute hashes instead of the built-in Python library used in earlier tutorials.
-
-Start by entering the @crunch_scripts@ directory of your Git working tree:
+Use the following command to create a new empty template using @arv pipeline_template create@:
<notextile>
-<pre><code>~$ <span class="userinput">cd <b>you</b>/crunch_scripts</span>
-</code></pre>
+<pre><code>~$ <span class="userinput">arv edit $(arv --format=uuid pipeline_template create --pipeline-template '{}') name components </span></code></pre>
</notextile>
-Next, using @nano@ or your favorite Unix text editor, create a new file called @run-md5sum.py@ in the @crunch_scripts@ directory.
-
-notextile. <pre>~/<b>you</b>/crunch_scripts$ <code class="userinput">nano run-md5sum.py</code></pre>
+* @--format=uuid@ option prints out just the unique identifier for the new template, instead of the entire template record (default)
-Add the following code to use the @md5sum@ program to compute the hash of each file in a collection:
+This will open the template record in an interactive text editor (as specified by $EDITOR or $VISUAL, otherwise defaults to @nano@) using @arv edit@. Now add the following content:
-<notextile> {% code 'run_md5sum_py' as python %} </notextile>
+<notextile>{% code 'tutorial_bwa_sortsam_pipeline' as javascript %}</notextile>
-Make the file executable:
+* @"name"@ is a human-readable name for the pipeline.
+* @"components"@ is a set of scripts or commands that make up the pipeline. Each component is given an identifier (@"bwa-mem"@ and @"SortSam"@) in this example).
+** Each entry in components @"components"@ is an Arvados job submission. For more information about individual jobs, see the "job object reference":{{site.baseurl}}/api/schema/Job.html and "job create method.":{{site.baseurl}}/api/methods/jobs.html#create
+* @"repository"@, @"script_version"@, and @"script"@ indicate that we intend to use the external @"run-command"@ tool wrapper that is part of the Arvados. These parameters are described in more detail in "Writing a script":tutorial-firstscript.html
+* @"output_is_persistent"@ indicates whether the output of the component is considered valuable. If this value is false (or not given), the output will be treated as intermediate data which may be eventually deleted to reclaim disk space.
+* @"runtime_constraints"@ describes runtime resource requirements for the component.
+** @"docker_image"@ specifies the "Docker":https://www.docker.com/ runtime environment in which to run the job. The Docker image @"arvados/jobs-java-bwa-samtools"@ supplied here has the Arvados SDK, Java runtime environment, bwa, and samtools installed.
+* @"script_parameters"@ describes the component parameters.
+** @"command"@ is the actual command line to invoke the @bwa@ and then @SortSam@. The notation @$()@ denotes macro substitution commands evaluated by the run-command tool wrapper.
+** @"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 $(...))@ evaluates to the supplied path with leading path portion and trailing filename extensions stripped
+** @"output_of"@ indicates that the @output@ of the @bwa-mem@ component should be used as the @"input"@ of @SortSam@. Arvados uses these dependencies between components to automatically determine the correct order to run them.
-notextile. <pre><code>~/<b>you</b>/crunch_scripts$ <span class="userinput">chmod +x run-md5sum.py</span></code></pre>
+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.
-Next, use Git to stage the file, commit, and push:
+h2. Running your pipeline
-<notextile>
-<pre><code>~/<b>you</b>/crunch_scripts$ <span class="userinput">git add run-md5sum.py</span>
-~/<b>you</b>/crunch_scripts$ <span class="userinput">git commit -m"run external md5sum program"</span>
-~/<b>you</b>/crunch_scripts$ <span class="userinput">git push origin master</span>
-</code></pre>
-</notextile>
+Your new pipeline template should appear at the top of the Workbench "pipeline templates":https://{{ 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
-You should now be able to run your new script using Crunch, with @"script"@ referring to our new @run-md5sum.py@ script.
-
-<notextile>
-<pre><code>~/<b>you</b>/crunch_scripts$ <span class="userinput">cat >~/the_pipeline <<EOF
-{
- "name":"Run external md5sum program",
- "components":{
- "do_hash":{
- "script":"run-md5sum.py",
- "script_parameters":{
- "input":{
- "required": true,
- "dataclass": "Collection"
- }
- },
- "repository":"$USER",
- "script_version":"master"
- }
- }
-}
-EOF
-</span>~/<b>you</b>/crunch_scripts$ <span class="userinput">arv pipeline_template create --pipeline-template "$(cat ~/the_pipeline)"</span>
-</code></pre>
-</notextile>
+Test data is available in the "Arvados Tutorial":https://{{ site.arvados_workbench_host }}/projects/qr1hi-j7d0g-u7zg1qdaowykd8d project:
-(Your shell should automatically fill in @$USER@ with your login name. The JSON that gets saved should have @"repository"@ pointed at your personal Git repository.)
+* Choose <i class="fa fa-fw fa-archive"></i> "Tutorial chromosome 19 reference (2463fa9efeb75e099685528b3b9071e0+438)":https://{{ 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)":https://{{ site.arvados_workbench_host }}/collections/3229739b505d2b878b62aed09895a55a+142 for the "sample" parameter
-Your new pipeline template will appear on the Workbench "Compute %(rarr)→% Pipeline templates":https://{{ site.arvados_workbench_host }}/pipeline_templates page. You can run the "pipeline using Workbench":tutorial-pipeline-workbench.html.
+For more information and examples for writing pipelines, see the "pipeline template reference":{{site.baseurl}}/api/schema/PipelineTemplate.html
projects / arvados.git / blobdiff