Merge branch 'master' into 2272-setup-user-in-workbench

[arvados.git] / doc / user / tutorials / tutorial-new-pipeline.html.textile.liquid

diff --git a/doc/user/tutorials/tutorial-new-pipeline.html.textile.liquid b/doc/user/tutorials/tutorial-new-pipeline.html.textile.liquid
index fe849a5cb47d1b95ccfb6f20dc82c579b1b8b8f7..a832434287aad6189796c7906e5e06bb20a32162 100644 (file)
--- a/doc/user/tutorials/tutorial-new-pipeline.html.textile.liquid
+++ b/doc/user/tutorials/tutorial-new-pipeline.html.textile.liquid
@@ -8,18 +8,21 @@ A pipeline in Arvados is a collection of crunch scripts, in which the output fro
 
 *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.
+
 h2. Create a new script
 
-Our second script will filter the output of @hash.py@ and only include hashes that start with 0.  Create a new script in @crunch_scripts/@ called @0-filter.py@:
+Our second script will filter the output of @hash.py@ and only include hashes that start with 0.  Create a new script in <notextile><code>~/<b>you</b>/crunch_scripts/</code></notextile> called @0-filter.py@:
 
 <notextile> {% code '0_filter_py' as python %} </notextile>
 
 Now add it to git:
 
 <notextile>
-<pre><code>$ <span class="userinput">git add 0-filter.py</span>
-$ <span class="userinput">git commit -m"zero filter"</span>
-$ <span class="userinput">git push origin master</span>
+<pre><code>~/<b>you</b>/crunch_scripts$ <span class="userinput">chmod +x 0-filter.py</span>
+~/<b>you</b>/crunch_scripts$ <span class="userinput">git add 0-filter.py</span>
+~/<b>you</b>/crunch_scripts$ <span class="userinput">git commit -m"zero filter"</span>
+~/<b>you</b>/crunch_scripts$ <span class="userinput">git push origin master</span>
 </code></pre>
 </notextile>
 
@@ -28,7 +31,7 @@ h2. Create a pipeline template
 Next, create a file that contains the pipeline definition:
 
 <notextile>
-<pre><code>$ <span class="userinput">cat &gt;the_pipeline &lt;&lt;EOF
+<pre><code>~/<b>you</b>/crunch_scripts$ <span class="userinput">cat &gt;~/the_pipeline &lt;&lt;EOF
 {
   "name":"Filter md5 hash values",
   "components":{
@@ -40,16 +43,20 @@ Next, create a file that contains the pipeline definition:
           "dataclass": "Collection"
         }
       },
-      "script_version":"you:master"
+      "repository":"$USER",
+      "script_version":"master",
+      "output_is_persistent":false
     },
-    "filter":{
+    "do_filter":{
       "script":"0-filter.py",
       "script_parameters":{
         "input":{
           "output_of":"do_hash"
         }
       },
-      "script_version":"you:master"
+      "repository":"$USER",
+      "script_version":"master",
+      "output_is_persistent":true
     }
   }
 }
@@ -57,14 +64,15 @@ EOF
 </span></code></pre>
 </notextile>
 
-* @"output_of"@ indicates that the @input@ of the @do_hash@ component is connected to the @output@ of @filter@.  This is a _dependency_.  Arvados uses the dependencies between jobs to automatically determine the correct order to run the jobs.
+* @"output_of"@ indicates that the @output@ of the @do_hash@ component should be used as the @"input"@ of @do_filter@.  Arvados uses these dependencies between jobs to automatically determine the correct order to run them.
+
+(Your shell should automatically fill in @$USER@ with your login name.  The JSON that gets saved should have @"repository"@ pointed at your personal 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 "$(cat the_pipeline)"</span>
+<pre><code>~/<b>you</b>/crunch_scripts$ <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)&rarr;% Compute %(rarr)&rarr;% Pipeline&nbsp;templates":http://{{ site.arvados_workbench_host }}/pipeline_instances page.
-
+Your new pipeline template will appear on the Workbench "Compute %(rarr)&rarr;% Pipeline&nbsp;templates":https://{{ site.arvados_workbench_host }}/pipeline_instances page.