5 title: "Writing a Crunch script"
9 h1. Writing a Crunch script
11 In this tutorial, we will write the "hash" script demonstrated in the first tutorial.
13 *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*
15 This tutorial uses *@you@* to denote your username. Replace *@you@* with your user name in all the following examples.
19 As discussed in the previous tutorial, all Crunch scripts are managed through the @git@ revision control system.
21 First, you should do some basic configuration for git (you only need to do this the first time):
24 <pre><code>~$ <span class="userinput">git config --global user.name "Your Name"</span>
25 ~$ <span class="userinput">git config --global user.email <b>you</b>@example.com</span></code></pre>
28 On the Arvados Workbench, navigate to _Compute %(rarr)→% Code repositories._ You should see two repositories, one named "arvados" (under the *name* column) and a second with your user name. Next to *name* is the column *push_url*. Copy the *push_url* cell associated with your repository. This should look like <notextile><code>git@git.{{ site.arvados_api_host }}:<b>you</b>.git</code></notextile>.
30 Next, on the Arvados virtual machine, clone your git repository:
33 <pre><code>~$ <span class="userinput">git clone git@git.{{ site.arvados_api_host }}:<b>you</b>.git</span>
34 Cloning into '<b>you</b>'...</code></pre>
37 This will create an git checkout in the directory called *@you@*.
39 {% include 'notebox_begin' %}
40 For more information about using @git@, try
42 notextile. <pre><code>$ <span class="userinput">man gittutorial</span></code></pre>
44 or <b>"click here to search Google for git tutorials":http://google.com/#q=git+tutorial</b>
45 {% include 'notebox_end' %}
47 h2. Creating a Crunch script
49 Start by entering the *@you@* directory created by @git clone@. Next create a subdirectory called @crunch_scripts@ and change to that directory:
52 <pre><code>~$ <span class="userinput">cd <b>you</b></span>
53 ~/<b>you</b>$ <span class="userinput">mkdir crunch_scripts</span>
54 ~/<b>you</b>$ <span class="userinput">cd crunch_scripts</span></code></pre>
57 Next, using @nano@ or your favorite Unix text editor, create a new file called @hash.py@ in the @crunch_scripts@ directory.
59 notextile. <pre>~/<b>you</b>/crunch_scripts$ <code class="userinput">nano hash.py</code></pre>
61 Add the following code to compute the md5 hash of each file in a collection:
63 <pre><code class="userinput">{% include 'tutorial_hash_script_py' %}</code></pre>
65 Make the file executable:
67 notextile. <pre><code>~/<b>you</b>/crunch_scripts$ <span class="userinput">chmod +x hash.py</span></code></pre>
69 {% include 'notebox_begin' %}
70 The below steps describe how to execute the script after committing changes to git. To test the script locally, please see the "debugging a crunch script":tutorial-job-debug.html page.
72 {% include 'notebox_end' %}
74 Next, add the file to @git@ staging. This tells @git@ that the file should be included on the next commit.
76 notextile. <pre><code>~/<b>you</b>/crunch_scripts$ <span class="userinput">git add hash.py</span></code></pre>
78 Next, commit your changes to git. All staged changes are recorded into the local @git@ repository:
81 <pre><code>~/<b>you</b>/crunch_scripts$ <span class="userinput">git commit -m"my first script"</span>
82 [master (root-commit) 27fd88b] my first script
83 1 file changed, 33 insertions(+)
84 create mode 100755 crunch_scripts/hash.py</code></pre>
87 Finally, upload your changes to the Arvados server:
90 <pre><code>~/<b>you</b>/crunch_scripts$ <span class="userinput">git push origin master</span>
91 Counting objects: 4, done.
92 Compressing objects: 100% (2/2), done.
93 Writing objects: 100% (4/4), 682 bytes, done.
94 Total 4 (delta 0), reused 0 (delta 0)
95 To git@git.qr1hi.arvadosapi.com:you.git
96 * [new branch] master -> master</code></pre>
99 You should now be able to run your script using Crunch, similar to how we did it in the "first tutorial.":tutorial-job1.html The field @"script_version"@ should be @you:master@ to tell Crunch to run the script at the head of the "master" git branch, which you just uploaded.
102 <pre><code>~/<b>you</b>/crunch_scripts$ <span class="userinput">cat >~/the_job <<EOF
105 "script_version": "you:master",
108 "input": "c1bad4b39ca5a924e481008009d94e32+210"
112 ~/<b>you</b>/crunch_scripts$ <span class="userinput">arv job create --job "$(cat ~/the_job)"</span>
115 "uuid":"qr1hi-xxxxx-xxxxxxxxxxxxxxx"
118 ~/<b>you</b>/crunch_scripts$ <span class="userinput">arv job get --uuid qr1hi-xxxxx-xxxxxxxxxxxxxxx</span>
121 "output":"880b55fb4470b148a447ff38cacdd952+54",
124 ~/<b>you</b>/crunch_scripts$ <span class="userinput">arv keep get 880b55fb4470b148a447ff38cacdd952+54/md5sum.txt</span>
125 44b8ae3fde7a8a88d2f7ebd237625b4f var-GS000016015-ASM.tsv.bz2
129 Next, "debugging a crunch script.":tutorial-job-debug.html