Merge branch 'master' into 2449-keep-write-blocks

[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 7b31e17818318f178da36b46562f65fc6ff89bd0..56b71c05eec10c68b48fee0b28821278be86b750 100644 (file)
--- a/doc/user/tutorials/running-external-program.html.textile.liquid
+++ b/doc/user/tutorials/running-external-program.html.textile.liquid
@@ -1,13 +1,9 @@
 ---
 layout: default
 navsection: userguide
-navmenu: Tutorials
-title: "Running external programs"
-
+title: "Using Crunch to run external programs"
 ...
 
-h1. Running external programs
-
 This tutorial demonstrates how to use Crunch to run an external program by writting a wrapper using the Python SDK.
 
 *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*
@@ -21,19 +17,19 @@ Start by entering the @crunch_scripts@ directory of your git repository:
 </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>
 
 Add the following code to use the @md5sum@ program to compute the hash of each file in a collection:
 
-<pre><code class="userinput">{% include 'run_md5sum_py' %}</code></pre>
+<notextile> {% code 'run_md5sum_py' as python %} </notextile>
 
 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>
@@ -42,30 +38,31 @@ 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>~/<b>you</b>/crunch_scripts$ <span class="userinput">cat &gt;~/the_job &lt;&lt;EOF
-{
- "script": "run-md5sum.py",
- "script_version": "you:master",
- "script_parameters":
- {
-  "input": "c1bad4b39ca5a924e481008009d94e32+210"
- }
-}
-EOF</span>
-~/<b>you</b>/crunch_scripts$ <span class="userinput">arv job create --job "$(cat the_job)"</span>
+<pre><code>~/<b>you</b>/crunch_scripts$ <span class="userinput">cat &gt;~/the_pipeline &lt;&lt;EOF
 {
- ...
- "uuid":"qr1hi-xxxxx-xxxxxxxxxxxxxxx"
- ...
-}
-~/<b>you</b>/crunch_scripts$ <span class="userinput">arv job get --uuid qr1hi-xxxxx-xxxxxxxxxxxxxxx</span>
-{
- ...
- "output":"4d164b1658c261b9afc6b479130016a3+54",
- ...
+  "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 "$(cat ~/the_pipeline)"</span>
 </code></pre>
 </notextile>
+
+(Your shell should automatically fill in @$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_instances page.  You can run the "pipeline using Workbench":tutorial-pipeline-workbench.html.