doc/user/tutorials/running-external-program.textile

   1 ---
   2 layout: default
   3 navsection: userguide
   4 navmenu: Tutorials
   5 title: "Running external programs"
   6 navorder: 18
   7 ...
   8
   9 h1. Running external programs
  10
  11 This tutorial demonstrates how to use Crunch to run an external program by writting a wrapper using the Python SDK.
  12
  13 *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*
  14
  15 In this tutorial, you will use the external program @md5sum@ to compute hashes instead of the built-in Python library used in earlier tutorials.
  16
  17 Start by entering the @crunch_scripts@ directory of your git repository:
  18
  19 <notextile>
  20 <pre><code>$ <span class="userinput">cd you/crunch_scripts</span>
  21 </code></pre>
  22 </notextile>
  23
  24 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:
  25
  26 <pre><code class="userinput">{% include run-md5sum.py %}</code></pre>
  27
  28 Make the file executable:
  29
  30 notextile. <pre><code>$ <span class="userinput">chmod +x run-md5sum.py</span></code></pre>
  31
  32 Next, add the file to @git@ staging, commit and push:
  33
  34 <notextile>
  35 <pre><code>$ <span class="userinput">git add run-md5sum.py</span>
  36 $ <span class="userinput">git commit -m"run external md5sum program"</span>
  37 $ <span class="userinput">git push origin master</span>
  38 </code></pre>
  39 </notextile>
  40
  41 You should now be able to run your new script using Crunch, with "script" referring to our new "run-md5sum.py" script.
  42
  43 <notextile>
  44 <pre><code>$ <span class="userinput">cat &gt;the_job &lt;&lt;EOF
  45 {
  46  "script": "run-md5sum.py",
  47  "script_version": "you:master",
  48  "script_parameters":
  49  {
  50   "input": "c1bad4b39ca5a924e481008009d94e32+210"
  51  }
  52 }
  53 EOF</span>
  54 $ <span class="userinput">arv -h job create --job "$(cat the_job)"</span>
  55 {
  56  ...
  57  "uuid":"qr1hi-xxxxx-xxxxxxxxxxxxxxx"
  58  ...
  59 }
  60 $ <span class="userinput">arv -h job get --uuid qr1hi-xxxxx-xxxxxxxxxxxxxxx</span>
  61 {
  62  ...
  63  "output":"4d164b1658c261b9afc6b479130016a3+54",
  64  ...
  65 }
  66 </code></pre>
  67 </notextile>