[ARVADOS] updated: 8089b2f5c97b1db9bd826a1b6488f1b060830def
git at public.curoverse.com
git at public.curoverse.com
Thu Aug 6 16:28:07 EDT 2015
Summary of changes:
.../running-external-program.html.textile.liquid | 17 ++++++++++++++++-
1 file changed, 16 insertions(+), 1 deletion(-)
via 8089b2f5c97b1db9bd826a1b6488f1b060830def (commit)
via 97f16e9b6ce0095a40b68781238550d066a15261 (commit)
via 43338e77fc9ac255511395d8a8b1ae4bb8c98577 (commit)
via bbf7272aa2b831102c47fc93f8966ec32e918205 (commit)
via 03d5c4df2f33c5bb2117c45869808fa018e855f1 (commit)
from 261fe4c689858952b19991e0055eda669ab144af (commit)
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commit 8089b2f5c97b1db9bd826a1b6488f1b060830def
Merge: 261fe4c 97f16e9
Author: Bryan Cosca <bcosc at curoverse.com>
Date: Thu Aug 6 16:27:11 2015 -0400
Merge branch '6858-job-re-run-documentation'
closes #6858
commit 97f16e9b6ce0095a40b68781238550d066a15261
Author: Bryan Cosca <bcosc at curoverse.com>
Date: Thu Aug 6 15:06:34 2015 -0400
6858: Fixed syntax and added notes to re-use the same hashes from previous runs
diff --git a/doc/user/tutorials/running-external-program.html.textile.liquid b/doc/user/tutorials/running-external-program.html.textile.liquid
index 687379b..35d54bd 100644
--- a/doc/user/tutorials/running-external-program.html.textile.liquid
+++ b/doc/user/tutorials/running-external-program.html.textile.liquid
@@ -54,15 +54,15 @@ For more information and examples for writing pipelines, see the "pipeline templ
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.
+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 which version control parameters should be tuned 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:
+* @"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*. Make sure you set this to the same version as the previous run that you are trying to reuse.
+* @"script_version"@ : The script_version is the commit hash of the git branch that the crunch script resides in. 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*.
+* @"docker_image"@ : This specifies the "Docker":https://www.docker.com/ runtime environment where jobs run their scripts. Docker version control is similar to git, and you can commit and push changes to your images. You must re-use the docker image hash from the previous run to use the same image. It can be found on the "Collection page":https://cloud.curoverse.com/collections/qr1hi-4zz18-dov6im679g3jr1n as the *Content address* or the *docker_image_locator* in a job's metadata.
commit 43338e77fc9ac255511395d8a8b1ae4bb8c98577
Author: Bryan Cosca <bcosc at curoverse.com>
Date: Thu Aug 6 14:22:31 2015 -0400
6858: 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*.
commit bbf7272aa2b831102c47fc93f8966ec32e918205
Author: Bryan Cosca <bcosc at curoverse.com>
Date: Thu Aug 6 11:54:42 2015 -0400
6858: Added note about job reproducibility and version control with arvados_sdk_version, script_version, and docker_image to Writing a Pipeline template
diff --git a/doc/user/tutorials/running-external-program.html.textile.liquid b/doc/user/tutorials/running-external-program.html.textile.liquid
index 3ed6ea6..6f1dae3 100644
--- a/doc/user/tutorials/running-external-program.html.textile.liquid
+++ b/doc/user/tutorials/running-external-program.html.textile.liquid
@@ -41,6 +41,16 @@ 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
commit 03d5c4df2f33c5bb2117c45869808fa018e855f1
Author: radhika <radhika at curoverse.com>
Date: Thu Aug 6 08:48:46 2015 -0400
6851: reorder install guide pages; right after api server, install workbench, shell server and standard objects.
diff --git a/doc/_config.yml b/doc/_config.yml
index ba071d5..3cd354b 100644
--- a/doc/_config.yml
+++ b/doc/_config.yml
@@ -150,12 +150,12 @@ navbar:
- install/install-manual-prerequisites.html.textile.liquid
- install/install-sso.html.textile.liquid
- install/install-api-server.html.textile.liquid
+ - install/install-workbench-app.html.textile.liquid
+ - install/install-shell-server.html.textile.liquid
+ - install/create-standard-objects.html.textile.liquid
- install/install-arv-git-httpd.html.textile.liquid
- install/install-keepstore.html.textile.liquid
- install/install-keepproxy.html.textile.liquid
- install/install-crunch-dispatch.html.textile.liquid
- install/install-compute-node.html.textile.liquid
- - install/install-shell-server.html.textile.liquid
- - install/create-standard-objects.html.textile.liquid
- - install/install-workbench-app.html.textile.liquid
- install/cheat_sheet.html.textile.liquid
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