layout: default
navsection: userguide
navmenu: Tutorials
-title: "Writing a pipeline"
+title: "Writing a script"
...
-In this tutorial, we will write the "hash" script demonstrated in the first tutorial.
+This tutorial demonstrates how to write crunch script using the Arvados Python SDK. The Arvados SDK supports access to advanced features not available using the @run-command@ wrapper, such as scheduling parallel tasks across nodes.
-*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*
+{% include 'tutorial_expectations' %}
-This tutorial uses *@you@* to denote your username. Replace *@you@* with your user name in all the following examples.
+This tutorial uses @$USER@ to denote your username. Replace @$USER@ 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 <b>you</b>@example.com</span></code></pre>
+~$ <span class="userinput">git config --global user.email $USER@example.com</span></code></pre>
</notextile>
-On the Arvados Workbench, navigate to "Compute %(rarr)→% Code repositories":http://{{site.arvados_workbench_host}}/repositories . You should see a repository with your user name listed in the *name* column. Next to *name* is the column *push_url*. Copy the *push_url* value associated with your repository. This should look like <notextile><code>git@git.{{ site.arvados_api_host }}:<b>you</b>.git</code></notextile>.
+On the Arvados Workbench, navigate to "Code repositories":https://{{site.arvados_workbench_host}}/repositories. You should see a repository with your user name listed in the *name* column. Next to *name* is the column *push_url*. Copy the *push_url* value associated with your repository. This should look like <notextile><code>git@git.{{ site.arvados_api_host }}:$USER.git</code></notextile>.
-Next, on the Arvados virtual machine, clone your git repository:
+Next, on the Arvados virtual machine, clone your Git repository:
<notextile>
-<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>
+<pre><code>~$ <span class="userinput">cd $HOME</span> # (or wherever you want to install)
+~$ <span class="userinput">git clone git@git.{{ site.arvados_api_host }}:$USER.git</span>
+Cloning into '$USER'...</code></pre>
</notextile>
-This will create an git checkout in the directory called *@you@*.
+This will create a Git repository in the directory called @$USER@ in your home directory. Say yes when prompted to continue with connection.
+Ignore any warning that you are cloning an empty repository.
{% include 'notebox_begin' %}
-For more information about using @git@, try
+For more information about using Git, try
notextile. <pre><code>$ <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>
+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 @$USER@ directory created by @git clone@. Next create a subdirectory called @crunch_scripts@ and change to that directory:
<notextile>
-<pre><code>~$ <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>
+<pre><code>~$ <span class="userinput">cd $USER</span>
+~/$USER$ <span class="userinput">mkdir crunch_scripts</span>
+~/$USER$ <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>~/<b>you</b>/crunch_scripts$ <code class="userinput">nano hash.py</code></pre>
+notextile. <pre>~/$USER/crunch_scripts$ <code class="userinput">nano hash.py</code></pre>
-Add the following code to compute the md5 hash of each file in a collection:
+Add the following code to compute the MD5 hash of each file in a collection:
<notextile> {% code 'tutorial_hash_script_py' as python %} </notextile>
Make the file executable:
-notextile. <pre><code>~/<b>you</b>/crunch_scripts$ <span class="userinput">chmod +x hash.py</span></code></pre>
+notextile. <pre><code>~/$USER/crunch_scripts$ <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 .
+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.
{% include 'notebox_end' %}
-Next, add the file to @git@ staging. This tells @git@ that the file should be included on the next commit.
+Next, add the file to the staging area. This tells @git@ that the file should be included on the next commit.
-notextile. <pre><code>~/<b>you</b>/crunch_scripts$ <span class="userinput">git add hash.py</span></code></pre>
+notextile. <pre><code>~/$USER/crunch_scripts$ <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:
+Next, commit your changes. All staged changes are recorded into the local git repository:
<notextile>
-<pre><code>~/<b>you</b>/crunch_scripts$ <span class="userinput">git commit -m"my first script"</span>
+<pre><code>~/$USER/crunch_scripts$ <span class="userinput">git commit -m"my first script"</span>
[master (root-commit) 27fd88b] my first script
- 1 file changed, 33 insertions(+)
+ 1 file changed, 45 insertions(+)
create mode 100755 crunch_scripts/hash.py</code></pre>
</notextile>
Finally, upload your changes to the Arvados server:
<notextile>
-<pre><code>~/<b>you</b>/crunch_scripts$ <span class="userinput">git push origin master</span>
+<pre><code>~/$USER/crunch_scripts$ <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.
Total 4 (delta 0), reused 0 (delta 0)
-To git@git.qr1hi.arvadosapi.com:you.git
+To git@git.qr1hi.arvadosapi.com:$USER.git
* [new branch] master -> master</code></pre>
</notextile>
Next, create a file that contains the pipeline definition:
<notextile>
-<pre><code>~/<b>you</b>/crunch_scripts$ <span class="userinput">cd ~</span>
+<pre><code>~/$USER/crunch_scripts$ <span class="userinput">cd ~</span>
~$ <span class="userinput">cat >the_pipeline <<EOF
{
"name":"My first pipeline",
"dataclass": "Collection"
}
},
- "script_version":"<b>you</b>:master"
+ "repository":"$USER",
+ "script_version":"master",
+ "output_is_persistent":true,
+ "runtime_constraints":{
+ "docker_image":"arvados/jobs"
+ }
}
}
}
</span></code></pre>
</notextile>
-* @cat@ is a standard Unix utility that simply copies standard 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)
-* @"script"@ specifies the name of the script to run. The script is searched for in the "crunch_scripts/" subdirectory of the @git@ checkout specified by @"script_version"@.
-* @"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, or in the form "repository:branch" (in which case it will take 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. You can access a list of available @git@ repositories on the Arvados workbench under "Compute %(rarr)→% Code repositories":http://{{site.arvados_workbench_host}}//repositories .
-* @"script_parameters"@ describes the parameters for the script. In this example, there is one parameter called @input@ which is @required@ and is a @Collection@.
+* @"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 "Code repositories":https://{{site.arvados_workbench_host}}/repositories.
+* @"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.
-Now, use @arv pipeline_template create@ tell Arvados about your pipeline template:
+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>
-Your new pipeline template will appear on the "Workbench %(rarr)→% Compute %(rarr)→% Pipeline templates":http://{{ site.arvados_workbench_host }}/pipeline_instances page. You can run the "pipeline using workbench":tutorial-pipeline-workbench.html
+Your new pipeline template will appear on the Workbench "Pipeline templates":https://{{ site.arvados_workbench_host }}/pipeline_templates page. You can run the "pipeline using Workbench":tutorial-pipeline-workbench.html.
+
+For more information and examples for writing pipelines, see the "pipeline template reference":{{site.baseurl}}/api/schema/PipelineTemplate.html
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