X-Git-Url: https://git.arvados.org/arvados.git/blobdiff_plain/0042e4b42d9f4d3900aefc68617cb28c5a61a522..ed0067ee9964c70f646a5f4f72c1302cc19c007c:/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 f13d1c8319..18f5f7d35f 100644 --- 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@: -
~$ arv edit $(arv --format=uuid pipeline_template create --pipeline-template '{}') name components 
+
~$ arv create pipeline_template
-* @--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: {% code 'tutorial_bwa_sortsam_pipeline' as javascript %} @@ -40,6 +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 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