4253: Users can manage their own repositories.

[arvados.git] / doc / user / tutorials / tutorial-submit-job.html.textile.liquid

diff --git a/doc/user/tutorials/tutorial-submit-job.html.textile.liquid b/doc/user/tutorials/tutorial-submit-job.html.textile.liquid
index 8be72a2365de7aadd9e669985605e44a2f4ba3fd..7cc4b885490b0fe54db4ee59d73cf1cc043ba45b 100644 (file)
--- a/doc/user/tutorials/tutorial-submit-job.html.textile.liquid
+++ b/doc/user/tutorials/tutorial-submit-job.html.textile.liquid
@@ -20,13 +20,13 @@ All Crunch scripts are managed through the Git revision control system.  Before
 ~$ <span class="userinput">git config --global user.email $USER@example.com</span></code></pre>
 </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 }}:$USER.git</code></notextile>.
+On the Arvados Workbench, navigate to "Code repositories":https://{{site.arvados_workbench_host}}/repositories.  You should see a repository with your user name listed in the *name* column.  Next to *name* is the column *push_url*.  Copy the *push_url* value associated with your repository.  This should look like <notextile><code>git@git.{{ site.arvados_api_host }}:$USER/$USER.git</code></notextile>.
 
 Next, on the Arvados virtual machine, clone your Git repository:
 
 <notextile>
 <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 }}:$USER.git</span>
+~$ <span class="userinput">git clone git@git.{{ site.arvados_api_host }}:$USER/$USER.git</span>
 Cloning into '$USER'...</code></pre>
 </notextile>
 
@@ -84,51 +84,26 @@ 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:$USER.git
+To git@git.qr1hi.arvadosapi.com:$USER/$USER.git
  * [new branch]      master -> master</code></pre>
 </notextile>
 
 h2. Create a pipeline template
 
-Next, create a file that contains the pipeline definition:
+Next, create a new template using @arv create pipeline_template@:
 
 <notextile>
-<pre><code>~/$USER/crunch_scripts$ <span class="userinput">cd ~</span>
-~$ <span class="userinput">cat &gt;the_pipeline &lt;&lt;EOF
-{
-  "name":"My md5 pipeline",
-  "components":{
-    "do_hash":{
-      "script":"hash.py",
-      "script_parameters":{
-        "input":{
-          "required": true,
-          "dataclass": "Collection"
-        }
-      },
-      "repository":"$USER",
-      "script_version":"master",
-      "output_is_persistent":true,
-      "runtime_constraints":{
-        "docker_image":"arvados/jobs-java-bwa-samtools"
-      }
-    }
-  }
-}
-EOF
-</span></code></pre>
+<pre><code>~$ <span class="userinput">arv create pipeline_template</span></code></pre>
 </notextile>
 
+In the editor, enter the following template:
+
+<notextile> {% code 'tutorial_submit_job' as javascript %} </notextile>
+
 * @"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@ 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>
+* @"runtime_constraints"@ describes the runtime environment required to run the job.  These are described in the "job record schema":{{site.baseurl}}/api/schema/Job.html
 
 h2. Running your pipeline