[ARVADOS] updated: f56323e1b8df158bc2fd41798298f6d3f25aa228

Thu Aug 6 14:22:41 EDT 2015

Summary of changes:
 .../running-external-program.html.textile.liquid   | 27 +++++++++++++---------
 1 file changed, 16 insertions(+), 11 deletions(-)

       via  f56323e1b8df158bc2fd41798298f6d3f25aa228 (commit)
      from  2f719adbd0eb4ce07fc2c7012bc1ce8df02e790b (commit)

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commit f56323e1b8df158bc2fd41798298f6d3f25aa228
Author: Bryan Cosca <bcosc at curoverse.com>
Date:   Thu Aug 6 14:22:31 2015 -0400

    Added new section 'Re-using your pipeline run' and moved all version control parameters there for ease of reading. Added more explanation of all parameters

diff --git a/doc/user/tutorials/running-external-program.html.textile.liquid b/doc/user/tutorials/running-external-program.html.textile.liquid
index 6f1dae3..687379b 100644
--- a/doc/user/tutorials/running-external-program.html.textile.liquid
+++ b/doc/user/tutorials/running-external-program.html.textile.liquid
@@ -24,7 +24,7 @@ This will open the template record in an interactive text editor (as specified b
 * @"repository"@, @"script_version"@, and @"script"@ indicate that we intend to use the external @"run-command"@ tool wrapper that is part of the Arvados.  These parameters are described in more detail in "Writing a script":tutorial-firstscript.html.
 * @"runtime_constraints"@ describes runtime resource requirements for the component.
 ** @"docker_image"@ specifies the "Docker":https://www.docker.com/ runtime environment in which to run the job.  The Docker image @"bcosc/arv-base-java"@ supplied here has the Java runtime environment, bwa, and samtools installed.
-** @"arvados_sdk_version"@ specifies a version of the Arvados SDK to load alongside the job's script.
+** @"arvados_sdk_version"@ specifies a version of the Arvados SDK to load alongside the job's script. The example uses 'master'. If you would like to use a specific version of the sdk, you can find it in the "Arvados Python sdk repository":https://arvados.org/projects/arvados/repository/revisions/master/show/sdk/python under *Latest revisions*.
 * @"script_parameters"@ describes the component parameters.
 ** @"command"@ is the actual command line to invoke the @bwa@ and then @SortSam at .  The notation @$()@ denotes macro substitution commands evaluated by the run-command tool wrapper.
 ** @"task.stdout"@ indicates that the output of this command should be captured to a file.
@@ -41,16 +41,6 @@ When using @run-command@, the tool should write its output to the current workin
 
 See the "run-command reference":{{site.baseurl}}/user/topics/run-command.html for more information about using @run-command at .
 
-*Note:* When trying to get job reproducibility without re-computation, you need to set these parameters to their specific hashes. Using a version such as master in @"arvados_sdk_version"@ will grab the latest version hash, which will allow Arvados to re-compute your job if the sdk gets updated.
-* @"arvados_sdk_version"@ : The latest version can be found on the "Arvados Python sdk repository":https://arvados.org/projects/arvados/repository/revisions/master/show/sdk/python under *Latest revisions*.
-* @"script_version"@ : The current version of your script in your git repository can be found by using the following command:
-
-<notextile>
-<pre><code>~$ <span class="userinput">git rev-parse HEAD</span></code></pre>
-</notextile>
-
-* @"docker_image"@ : The docker image hash used is found on the "Collection page":https://cloud.curoverse.com/collections/qr1hi-4zz18-dov6im679g3jr1n as the *Content address*.
-
 h2. Running your pipeline
 
 Your new pipeline template should appear at the top of the Workbench "pipeline templates":{{site.arvados_workbench_host}}/pipeline_templates page.  You can run your pipeline "using Workbench":tutorial-pipeline-workbench.html or the "command line.":{{site.baseurl}}/user/topics/running-pipeline-command-line.html
@@ -61,3 +51,18 @@ Test data is available in the "Arvados Tutorial":{{site.arvados_workbench_host}}
 * Choose <i class="fa fa-fw fa-archive"></i> "Tutorial sample exome (3229739b505d2b878b62aed09895a55a+142)":{{site.arvados_workbench_host}}/collections/3229739b505d2b878b62aed09895a55a+142 for the "sample" parameter
 
 For more information and examples for writing pipelines, see the "pipeline template reference":{{site.baseurl}}/api/schema/PipelineTemplate.html
+
+h2. Re-using your pipeline run
+
+Arvados allows users to re-use jobs that have the same inputs in order to save computing time and resources. Users are able to change a job downstream without re-computing earlier jobs. This section shows what parameters you need to version control in order to make sure Arvados will not re-compute your jobs. 
+
+Note: Job reuse can only happen if all input collections do not change.
+
+* @"arvados_sdk_version"@ : The arvados_sdk_version parameter is used to download the specific version of the Arvados sdk into the docker image. The latest version can be found in the "Arvados Python sdk repository":https://arvados.org/projects/arvados/repository/revisions/master/show/sdk/python under *Latest revisions*.
+* @"script_version"@ : The script_version is the commit hash of the git branch that the crunch script resides. This information can be found in your git repository by using the following command:
+
+<notextile>
+<pre><code>~$ <span class="userinput">git rev-parse HEAD</span></code></pre>
+</notextile>
+
+* @"docker_image"@ : This specifies the "Docker":https://www.docker.com/ runtime environment where job's run their scripts. Docker version control is similar to git, you can commit and push changes to your images. In order to version control your docker image on arvados, you must use the docker image hash which is found on the "Collection page":https://cloud.curoverse.com/collections/qr1hi-4zz18-dov6im679g3jr1n as the *Content address*.

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