Merge branch 'master' into 2380-ssh-doc

[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 be257f858988aa6babb431585f311e020eeb6037..da6df59c4d279b9ee739f51aee5f55e89aa6f89e 100644 (file)
--- a/doc/user/tutorials/running-external-program.html.textile.liquid
+++ b/doc/user/tutorials/running-external-program.html.textile.liquid
@@ -10,14 +10,14 @@ This tutorial demonstrates how to use Crunch to run an external program by writt
 
 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 repository:
+Start by entering the @crunch_scripts@ directory of your Git working tree:
 
 <notextile>
 <pre><code>~$ <span class="userinput">cd <b>you</b>/crunch_scripts</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.  
+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>
 
@@ -29,7 +29,7 @@ Make the file executable:
 
 notextile. <pre><code>~/<b>you</b>/crunch_scripts$ <span class="userinput">chmod +x run-md5sum.py</span></code></pre>
 
-Next, add the file to @git@ staging, commit and push:
+Next, use Git to stage the file, commit, and push:
 
 <notextile>
 <pre><code>~/<b>you</b>/crunch_scripts$ <span class="userinput">git add run-md5sum.py</span>
@@ -38,10 +38,10 @@ Next, add the file to @git@ staging, commit and push:
 </code></pre>
 </notextile>
 
-You should now be able to run your new script using Crunch, with "script" referring to our new "run-md5sum.py" script.
+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>$ <span class="userinput">cat &gt;the_pipeline &lt;&lt;EOF
+<pre><code>~/<b>you</b>/crunch_scripts$ <span class="userinput">cat &gt;~/the_pipeline &lt;&lt;EOF
 {
   "name":"Run external md5sum program",
   "components":{
@@ -53,17 +53,16 @@ You should now be able to run your new script using Crunch, with "script" referr
           "dataclass": "Collection"
         }
       },
-      "script_version":"you:master"
+      "repository":"$USER",
+      "script_version":"master"
     }
   }
 }
 EOF
-</span></code></pre>
-</notextile>
-
-<notextile>
-<pre><code>$ <span class="userinput">arv pipeline_template create --pipeline-template "$(cat the_pipeline)"</span>
+</span>~/<b>you</b>/crunch_scripts$ <span class="userinput">arv pipeline_template create --pipeline-template "$(cat ~/the_pipeline)"</span>
 </code></pre>
 </notextile>
 
-Your new pipeline template will appear on the "Workbench %(rarr)&rarr;% Compute %(rarr)&rarr;% Pipeline&nbsp;templates":http://{{ site.arvados_workbench_host }}/pipeline_instances page.  You can run the "pipeline using workbench":tutorial-pipeline-workbench.html
+(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.)
+
+Your new pipeline template will appear on the Workbench "Compute %(rarr)&rarr;% Pipeline&nbsp;templates":https://{{ site.arvados_workbench_host }}/pipeline_templates page.  You can run the "pipeline using Workbench":tutorial-pipeline-workbench.html.