+++ /dev/null
----
-layout: default
-navsection: userguide
-navmenu: Tutorials
-title: "Writing a Crunch script"
-navorder: 13
-...
-
-h1. Writing a Crunch script
-
-In this tutorial, we will write the "hash" script demonstrated in the first tutorial.
-
-*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 uses _you_ to denote your username. Replace _you_ with your user name in all the following examples.
-
-h2. Setting up Git
-
-As discussed in the previous tutorial, all Crunch scripts are managed through the @git@ revision control system.
-
-First, you should do some basic configuration for git (you only need to do this the first time):
-
-<notextile>
-<pre><code>$ <span class="userinput">git config --global user.name "Your Name"</span>
-$ <span class="userinput">git config --global user.email you@example.com</span></code></pre>
-</notextile>
-
-On the Arvados Workbench, navigate to _Access %(rarr)→% 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 <code>git@git.{{ site.arvados_api_host }}:you.git</code>.
-
-Next, on the Arvados virtual machine, clone your git repository:
-
-<notextile>
-<pre><code>$ <span class="userinput">git clone git@git.{{ site.arvados_api_host }}:you.git</span>
-Cloning into 'you'...</code></pre>
-</notextile>
-
-This will create an git checkout in the directory called @you@.
-
-{% include notebox-begin.html %}
-For more information about using @git@, try
-
-notextile. <pre><code>$ <span class="userinput">man gittutorial</span></code></pre>
-
-or <b>"click here to search Google for git tutorials":http://google.com/#q=git+tutorial</b>
-{% include notebox-end.html %}
-
-h2. Creating a Crunch script
-
-Start by entering the @you@ directory created by @git clone@. Next create a subdirectory called @crunch_scripts@ and change to that directory:
-
-<notextile>
-<pre><code>$ <span class="userinput">cd you</span>
-$ <span class="userinput">mkdir crunch_scripts</span>
-$ <span class="userinput">cd crunch_scripts</span></code></pre>
-</notextile>
-
-Next, using @nano@ or your favorite Unix text editor, create a new file called @hash.py@ in the @crunch_scripts@ directory.
-
-notextile. <pre>$ <code class="userinput">nano hash.py</code></pre>
-
-Add the following code to compute the md5 hash of each file in a collection:
-
-<pre><code class="userinput">{% include tutorial_hash_script.py %}</code></pre>
-
-Make the file executable:
-
-notextile. <pre><code>$ <span class="userinput">chmod +x hash.py</span></code></pre>
-
-Next, add the file to @git@ staging. This tells @git@ that the file should be included on the next commit.
-
-notextile. <pre><code>$ <span class="userinput">git add hash.py</span></code></pre>
-
-Next, commit your changes to git. All staged changes are recorded into the local @git@ repository:
-
-<notextile>
-<pre><code>$ <span class="userinput">git commit -m"my first script"</span>
-[master (root-commit) 27fd88b] my first script
- 1 file changed, 33 insertions(+)
- create mode 100755 crunch_scripts/hash.py</code></pre>
-</notextile>
-
-Finally, upload your changes to the Arvados server:
-
-<notextile>
-<pre><code>$ <span class="userinput">git push origin master</span>
-Counting objects: 4, done.
-Compressing objects: 100% (2/2), done.
-Writing objects: 100% (4/4), 682 bytes, done.
-Total 4 (delta 0), reused 0 (delta 0)
-To git@git.qr1hi.arvadosapi.com:you.git
- * [new branch] master -> master</code></pre>
-</notextile>
-
-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.
-
-<notextile>
-<pre><code>$ <span class="userinput">cat >the_job <<EOF
-{
- "script": "hash.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":"880b55fb4470b148a447ff38cacdd952+54",
- ...
-}
-$ <span class="userinput">arv keep get 880b55fb4470b148a447ff38cacdd952+54/md5sum.txt</span>
-44b8ae3fde7a8a88d2f7ebd237625b4f var-GS000016015-ASM.tsv.bz2
-</code></pre>
-</notextile>
-
-Next, "debugging a crunch script.":tutorial-job-debug.html
projects / arvados.git / blobdiff
