h2. Setting up Git
-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):
+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>
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:
+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>
+<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 }}:<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 a Git repository in the directory called *@you@* 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 *"search Google for git tutorials":http://google.com/#q=git+tutorial*.
+or *"search Google for Git tutorials":http://google.com/#q=git+tutorial*.
{% include 'notebox_end' %}
h2. Creating a Crunch script
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:
+Add the following code to compute the MD5 hash of each file in a collection:
<notextile> {% code 'tutorial_hash_script_py' as python %} </notextile>
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.
+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>
-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>
[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>
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:<b>you</b>.git
* [new branch] master -> master</code></pre>
</notextile>
* @"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 @$USER@ with your login name, so that the final JSON has @"repository"@ pointed at your personal git repository.
-* @"script_version"@ specifies the version of the script that you wish to run. This can be in the form of an explicit git revision hash, a tag, or a branch (in which case it will use the HEAD of the specified branch). Arvados logs the script version that was used in the run, enabling you to go back and re-run any past job with the guarantee that the exact same code will be used as was used in the previous run.
-* @"script"@ specifies the filename of the script to run. Crunch expects to find this in the @crunch_scripts/@ subdirectory of the git repository.
+* @"repository"@ is the name of a git repository to search for the script version. You can access a list of available git repositories on the Arvados Workbench under "Compute %(rarr)→% Code repositories":https://{{site.arvados_workbench_host}}/repositories. Your shell should automatically fill in @$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.
</notextile>
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.
+
+For more information and examples for writing pipelines, see the "pipeline template reference":{{site.baseurl}}/api/schema/PipelineTemplate.html
projects / arvados.git / blobdiff