[ARVADOS] updated: 6ce66b16c069c6176dca37bbdc275cb286a08dab
git at public.curoverse.com
git at public.curoverse.com
Thu Oct 9 13:21:32 EDT 2014
Summary of changes:
.../running-external-program.html.textile.liquid | 10 +++---
.../tutorial-new-pipeline.html.textile.liquid | 10 +++---
.../tutorial-submit-job.html.textile.liquid | 38 ++++------------------
3 files changed, 16 insertions(+), 42 deletions(-)
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from 9dd2519aa44d751e6f0144226058dc5a98e4bcb5 (commit)
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commit 6ce66b16c069c6176dca37bbdc275cb286a08dab
Author: Peter Amstutz <peter.amstutz at curoverse.com>
Date: Thu Oct 9 13:21:27 2014 -0400
3656: Documentation updated to use "arv create".
diff --git a/doc/user/tutorials/running-external-program.html.textile.liquid b/doc/user/tutorials/running-external-program.html.textile.liquid
index f13d1c8..debe1db 100644
--- a/doc/user/tutorials/running-external-program.html.textile.liquid
+++ b/doc/user/tutorials/running-external-program.html.textile.liquid
@@ -8,15 +8,13 @@ This tutorial demonstrates how to construct a two stage pipeline template that u
{% include 'tutorial_expectations' %}
-Use the following command to create a new empty template using @arv pipeline_template create@:
+Use the following command to create a new empty template using @arv create pipeline_template@:
<notextile>
-<pre><code>~$ <span class="userinput">arv edit $(arv --format=uuid pipeline_template create --pipeline-template '{}') name components </span></code></pre>
+<pre><code>~$ <span class="userinput">arv create pipeline_template</span></code></pre>
</notextile>
-* @--format=uuid@ option prints out just the unique identifier for the new template, instead of the entire template record (default)
-
-This will open the template record in an interactive text editor (as specified by $EDITOR or $VISUAL, otherwise defaults to @nano@) using @arv edit at . Now add the following content:
+This will open the template record in an interactive text editor (as specified by $EDITOR or $VISUAL, otherwise defaults to @nano@). Now add the following content:
<notextile>{% code 'tutorial_bwa_sortsam_pipeline' as javascript %}</notextile>
@@ -40,6 +38,8 @@ This will open the template record in an interactive text editor (as specified b
When using @run-command@, the tool should write its output to the current working directory. The output will be automatically uploaded to Keep when the job completes.
+See the "run-command reference":{{site.baseurl}}/user/topics/run-command.html for more information about using @run-command at .
+
h2. Running your pipeline
Your new pipeline template should appear at the top of the Workbench "pipeline templates":https://{{ 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
diff --git a/doc/user/tutorials/tutorial-new-pipeline.html.textile.liquid b/doc/user/tutorials/tutorial-new-pipeline.html.textile.liquid
index 83303ad..fa8ee44 100644
--- a/doc/user/tutorials/tutorial-new-pipeline.html.textile.liquid
+++ b/doc/user/tutorials/tutorial-new-pipeline.html.textile.liquid
@@ -9,19 +9,17 @@ A pipeline in Arvados is a collection of crunch scripts, in which the output fro
{% include 'tutorial_expectations' %}
-First, use @arv pipeline_template create@ to create a new empty template. The @--format=uuid@ option will print out the unique identifier for the new template:
+First, use @arv create pipeline_template@ to create a new empty template. This will open the template record in an interactive text editor (as specified by $EDITOR or $VISUAL, otherwise defaults to @nano@).
<notextile>
-<pre><code>~$ <span class="userinput">arv --format=uuid pipeline_template create --pipeline-template '{}'</span>
-qr1hi-p5p6p-wt1vdhkezgx7g2k
-</span></code></pre>
+<pre><code>~$ <span class="userinput">arv create pipeline_template</span>
+</code></pre>
</notextile>
-Next, use @arv edit@ to edit the template. This will open the template record in an interactive text editor (as specified by $EDITOR or $VISUAL, otherwise defaults to @nano@). Replace the empty fields with the following content:
+Replace the empty fields with the following content:
<notextile>{% code 'tutorial_bwa_pipeline' as javascript %}</notextile>
-
Your new pipeline template will appear on the Workbench "Pipeline templates":https://{{ site.arvados_workbench_host }}/pipeline_templates page.
For more information and examples for writing pipelines, see the "pipeline template reference":{{site.baseurl}}/api/schema/PipelineTemplate.html
diff --git a/doc/user/tutorials/tutorial-submit-job.html.textile.liquid b/doc/user/tutorials/tutorial-submit-job.html.textile.liquid
index 10abdf0..fc77e5c 100644
--- a/doc/user/tutorials/tutorial-submit-job.html.textile.liquid
+++ b/doc/user/tutorials/tutorial-submit-job.html.textile.liquid
@@ -90,44 +90,20 @@ To git at git.qr1hi.arvadosapi.com:$USER.git
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 >the_pipeline <<EOF
-{
- "name":"My md5 pipeline",
- "components":{
- "do_hash":{
- "script":"hash.py",
- "script_parameters":{
- "input":{
- "required": true,
- "dataclass": "Collection"
- }
- },
- "repository":"$USER",
- "script_version":"master",
- "runtime_constraints":{
- "docker_image":"arvados/jobs-java-bwa-samtools"
- }
- }
- }
-}
-EOF
-</span></code></pre>
+<pre><code>~$ <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
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