refs 5930: misc. small documentation fixes

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

diff --git a/doc/user/tutorials/running-external-program.html.textile.liquid b/doc/user/tutorials/running-external-program.html.textile.liquid
index 3b9cd165f28562bcafc08db33aa26e481ebb2118..18f5f7d35f75eabeb2c45be8744846572bc7d548 100644 (file)
--- a/doc/user/tutorials/running-external-program.html.textile.liquid
+++ b/doc/user/tutorials/running-external-program.html.textile.liquid
@@ -8,15 +8,13 @@ This tutorial demonstrates how to construct a two stage pipeline template that u
 
 {% include 'tutorial_expectations' %}
 
-Use the following command to create a new empty template using @arv pipeline_template create@:
+Use the following command to create an empty template using @arv create pipeline_template@:
 
 <notextile>
-<pre><code>~$ <span class="userinput">arv edit $(arv --format=uuid pipeline_template create --pipeline-template '{}') name components </span></code></pre>
+<pre><code>~$ <span class="userinput">arv create pipeline_template</span></code></pre>
 </notextile>
 
-* @--format=uuid@ option prints out just the unique identifier for the new template, instead of the entire template record (default)
-
-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:
+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>
 
@@ -24,7 +22,6 @@ This will open the template record in an interactive text editor (as specified b
 * @"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.
@@ -41,6 +38,8 @@ This will open the template record in an interactive text editor (as specified b
 
 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":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