Merge branch 'master' into 1971-show-image-thumbnails

[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 e2860132470ed55f6d4331ccf93b0583cfd15666..56b71c05eec10c68b48fee0b28821278be86b750 100644 (file)
--- a/doc/user/tutorials/running-external-program.html.textile.liquid
+++ b/doc/user/tutorials/running-external-program.html.textile.liquid
@@ -1,67 +1,68 @@
 ---
 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.basedoc}}/user/getting_started/ssh-access.html#login, and have a "working environment.":{{site.basedoc}}/user/getting_started/check-environment.html*
+*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*
 
 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:
 
 <notextile>
-<pre><code>$ <span class="userinput">cd you/crunch_scripts</span>
+<pre><code>~$ <span class="userinput">cd <b>you</b>/crunch_scripts</span>
 </code></pre>
 </notextile>
- 
-Next, using your favorite text editor, create a new file called @run-md5sum.py@ in the @crunch_scripts@ directory.  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>
+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:
+
+<notextile> {% code 'run_md5sum_py' as python %} </notextile>
 
 Make the file executable:
 
-notextile. <pre><code>$ <span class="userinput">chmod +x run-md5sum.py</span></code></pre>
+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>$ <span class="userinput">git add run-md5sum.py</span>
-$ <span class="userinput">git commit -m"run external md5sum program"</span>
-$ <span class="userinput">git push origin master</span>
+<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>
 
-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_job &lt;&lt;EOF
+<pre><code>~/<b>you</b>/crunch_scripts$ <span class="userinput">cat &gt;~/the_pipeline &lt;&lt;EOF
 {
- "script": "run-md5sum.py",
- "script_version": "you:master",
- "script_parameters":
- {
-  "input": "c1bad4b39ca5a924e481008009d94e32+210"
- }
-}
-EOF</span>
-$ <span class="userinput">arv -h job create --job "$(cat the_job)"</span>
-{
- ...
- "uuid":"qr1hi-xxxxx-xxxxxxxxxxxxxxx"
- ...
-}
-$ <span class="userinput">arv -h 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.