layout: default
navsection: userguide
navmenu: Tutorials
-title: "Writing a Crunch script"
-
+title: "Writing a pipeline"
...
-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 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*
-This tutorial uses _you_ to denote your username. Replace _you_ with your user name in all the following examples.
+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):
+All Crunch scripts are managed through the @git@ revision control system. Before you start using git, you should do some basic configuration (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>
+<pre><code>~$ <span class="userinput">git config --global user.name "Your Name"</span>
+~$ <span class="userinput">git config --global user.email <b>you</b>@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>.
+On the Arvados Workbench, navigate to "Compute %(rarr)→% Code repositories":https://{{site.arvados_workbench_host}}/repositories. You should see a repository with your user name listed in the *name* column. Next to *name* is the column *push_url*. Copy the *push_url* value associated with your repository. This should look like <notextile><code>git@git.{{ site.arvados_api_host }}:<b>you</b>.git</code></notextile>.
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>
+<pre><code>~$ <span class="userinput">git clone git@git.{{ site.arvados_api_host }}:<b>you</b>.git</span>
+Cloning into '<b>you</b>'...</code></pre>
</notextile>
-This will create an git checkout in the directory called @you@.
+This will create an git checkout in the directory called *@you@*.
-{% include 'notebox-begin' %}
+{% include 'notebox_begin' %}
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' %}
+or *"search Google for git tutorials":http://google.com/#q=git+tutorial*.
+{% include 'notebox_end' %}
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:
+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>
+<pre><code>~$ <span class="userinput">cd <b>you</b></span>
+~/<b>you</b>$ <span class="userinput">mkdir crunch_scripts</span>
+~/<b>you</b>$ <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>
+notextile. <pre>~/<b>you</b>/crunch_scripts$ <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>
+<notextile> {% code 'tutorial_hash_script_py' as python %} </notextile>
Make the file executable:
-notextile. <pre><code>$ <span class="userinput">chmod +x hash.py</span></code></pre>
+notextile. <pre><code>~/<b>you</b>/crunch_scripts$ <span class="userinput">chmod +x hash.py</span></code></pre>
+
+{% include 'notebox_begin' %}
+The steps below describe how to execute the script after committing changes to git. To run a script locally for testing, please see "debugging a crunch script":{{site.baseurl}}/user/topics/tutorial-job-debug.html.
-Next, add the file to @git@ staging. This tells @git@ that the file should be included on the next commit.
+{% include 'notebox_end' %}
-notextile. <pre><code>$ <span class="userinput">git add 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.
-Next, commit your changes to git. All staged changes are recorded into the local @git@ repository:
+notextile. <pre><code>~/<b>you</b>/crunch_scripts$ <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>
+<pre><code>~/<b>you</b>/crunch_scripts$ <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>
Finally, upload your changes to the Arvados server:
<notextile>
-<pre><code>$ <span class="userinput">git push origin master</span>
+<pre><code>~/<b>you</b>/crunch_scripts$ <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.
* [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.
+h2. Create a pipeline template
+
+Next, create a file that contains the pipeline definition:
<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 "$(cat the_job)"</span>
+<pre><code>~/<b>you</b>/crunch_scripts$ <span class="userinput">cd ~</span>
+~$ <span class="userinput">cat >the_pipeline <<EOF
{
- ...
- "uuid":"qr1hi-xxxxx-xxxxxxxxxxxxxxx"
- ...
+ "name":"My first pipeline",
+ "components":{
+ "do_hash":{
+ "script":"hash.py",
+ "script_parameters":{
+ "input":{
+ "required": true,
+ "dataclass": "Collection"
+ }
+ },
+ "repository":"$USER",
+ "script_version":"master",
+ "output_is_persistent":true
+ }
+ }
}
-$ <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
+EOF
+</span></code></pre>
+</notextile>
+
+* @cat@ is a standard Unix utility that writes a sequence of input to standard output.
+* @<<EOF@ tells the shell to direct the following lines into the standard input for @cat@ up until it sees the line @EOF@.
+* @>the_pipeline@ redirects standard output to a file called @the_pipeline@.
+* @"name"@ is a human-readable name for the pipeline.
+* @"components"@ is a set of scripts that make up the pipeline.
+* The component is listed with a human-readable name (@"do_hash"@ in this example).
+* @"repository"@ is the name of a git repository to search for the script version. You can access a list of available git repositories on the Arvados Workbench under "Compute %(rarr)→% Code repositories":https://{{site.arvados_workbench_host}}/repositories. Your shell should automatically fill in @$USER@ with your login name, so that the final JSON has @"repository"@ pointed at your personal git repository.
+* @"script_version"@ specifies the version of the script that you wish to run. This can be in the form of an explicit git revision hash, a tag, or a branch (in which case it will use the HEAD of the specified branch). Arvados logs the script version that was used in the run, enabling you to go back and re-run any past job with the guarantee that the exact same code will be used as was used in the previous run.
+* @"script"@ specifies the filename of the script to run. Crunch expects to find this in the @crunch_scripts/@ subdirectory of the git repository.
+* @"script_parameters"@ describes the parameters for the script. In this example, there is one parameter called @input@ which is @required@ and is a @Collection@.
+* @"output_is_persistent"@ indicates whether the output of the job is considered valuable. If this value is false (or not given), the output will be treated as intermediate data and eventually deleted to reclaim disk space.
+
+Now, use @arv pipeline_template create@ to register your pipeline template in Arvados:
+
+<notextile>
+<pre><code>~$ <span class="userinput">arv pipeline_template create --pipeline-template "$(cat the_pipeline)"</span>
</code></pre>
</notextile>
-Next, "debugging a crunch script.":tutorial-job-debug.html
+Your new pipeline template will appear on the Workbench "Compute %(rarr)→% Pipeline templates":https://{{ site.arvados_workbench_host }}/pipeline_instances page. You can run the "pipeline using Workbench":tutorial-pipeline-workbench.html.
projects / arvados.git / blobdiff