X-Git-Url: https://git.arvados.org/arvados.git/blobdiff_plain/a22d6e6bf03c6f274237f775a4c02122c9ce38ef..b727cb3c8c32389f03e6ae71ad128c518a2c2a8c:/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 fc77e5cdc0..ff78aabb6a 100644
--- a/doc/user/tutorials/tutorial-submit-job.html.textile.liquid
+++ b/doc/user/tutorials/tutorial-submit-job.html.textile.liquid
@@ -4,6 +4,13 @@ navsection: userguide
navmenu: Tutorials
title: "Running on an Arvados cluster"
...
+{% comment %}
+Copyright (C) The Arvados Authors. All rights reserved.
+
+SPDX-License-Identifier: CC-BY-SA-3.0
+{% endcomment %}
+
+{% include 'pipeline_deprecation_notice' %}
This tutorial demonstrates how to create a pipeline to run your crunch script on an Arvados cluster. Cluster jobs can scale out to multiple nodes, and use @git@ and @docker@ to store the complete system snapshot required to achieve reproducibilty.
@@ -11,49 +18,25 @@ This tutorial demonstrates how to create a pipeline to run your crunch script on
This tutorial uses @$USER@ to denote your username. Replace @$USER@ with your user name in all the following examples.
-h2. Setting up Git
-
-All Crunch scripts are managed through the Git revision control system. Before you start using Git, you should do some basic configuration (you only need to do this the first time):
-
-
-~$ git config --global user.name "Your Name"
-~$ git config --global user.email $USER@example.com
-
-
-On the Arvados Workbench, navigate to "Code repositories":https://{{site.arvados_workbench_host}}/repositories. You should see a repository with your user name listed in the *name* column. Next to *name* is the column *push_url*. Copy the *push_url* value associated with your repository. This should look like git@git.{{ site.arvados_api_host }}:$USER.git.
-
-Next, on the Arvados virtual machine, clone your Git repository:
-
-
-~$ cd $HOME # (or wherever you want to install)
-~$ git clone git@git.{{ site.arvados_api_host }}:$USER.git
-Cloning into '$USER'...
-
-
-This will create a Git repository in the directory called @$USER@ in your home directory. Say yes when prompted to continue with connection.
-Ignore any warning that you are cloning an empty repository.
-
-{% include 'notebox_begin' %}
-For more information about using Git, try
+Also, this tutorial uses the @tutorial@ arvados repository created in "Adding a new arvados repository":add-new-repository.html as the example repository.
-notextile. $ man gittutorial
+h2. Clone Arvados repository
-or *"search Google for Git tutorials":http://google.com/#q=git+tutorial*.
-{% include 'notebox_end' %}
+Please clone the *tutorial* repository using the instructions from "Working with Arvados git repository":git-arvados-guide.html, if you have not yet cloned already.
h2. Creating a Crunch script
-Start by entering the @$USER@ directory created by @git clone@. Next create a subdirectory called @crunch_scripts@ and change to that directory:
+Start by entering the @tutorial@ directory created by @git clone@. Next, create a subdirectory called @crunch_scripts@ and change to that directory:
-~$ cd $USER
-~/$USER$ mkdir crunch_scripts
-~/$USER$ cd crunch_scripts
+>~$ cd tutorial
+~/tutorial$ mkdir crunch_scripts
+~/tutorial$ cd crunch_scripts
Next, using @nano@ or your favorite Unix text editor, create a new file called @hash.py@ in the @crunch_scripts@ directory.
-notextile. ~/$USER/crunch_scripts$ nano hash.py
+notextile. ~/tutorial/crunch_scripts$ nano hash.py
Add the following code to compute the MD5 hash of each file in a collection (if you already completed "Writing a Crunch script":tutorial-firstscript.html you can just copy the @hash.py@ file you created previously.)
@@ -61,16 +44,16 @@ Add the following code to compute the MD5 hash of each file in a collection (if
Make the file executable:
-notextile. ~/$USER/crunch_scripts$ chmod +x hash.py
+notextile. ~/tutorial/crunch_scripts$ chmod +x hash.py
Next, add the file to the staging area. This tells @git@ that the file should be included on the next commit.
-notextile. ~/$USER/crunch_scripts$ git add hash.py
+notextile. ~/tutorial/crunch_scripts$ git add hash.py
Next, commit your changes. All staged changes are recorded into the local git repository:
-~/$USER/crunch_scripts$ git commit -m"my first script"
+~/tutorial/crunch_scripts$ git commit -m "my first script"
[master (root-commit) 27fd88b] my first script
1 file changed, 45 insertions(+)
create mode 100755 crunch_scripts/hash.py
@@ -79,12 +62,12 @@ Next, commit your changes. All staged changes are recorded into the local git r
Finally, upload your changes to the Arvados server:
-~/$USER/crunch_scripts$ git push origin master
+~/tutorial/crunch_scripts$ git push origin master
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/tutorial.git
* [new branch] master -> master
@@ -100,13 +83,13 @@ In the editor, enter the following template:
{% code 'tutorial_submit_job' as javascript %}
-* @"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.
+* @"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 in the *Repositories* page using the top navigation menu icon.
* @"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.
-* @"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
+* @"runtime_constraints"@ describes the runtime environment required to run the job. These are described in the "job record schema":{{site.baseurl}}/api/methods/jobs.html
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
+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-workflow-workbench.html or the "command line.":{{site.baseurl}}/user/topics/running-pipeline-command-line.html
-For more information and examples for writing pipelines, see the "pipeline template reference":{{site.baseurl}}/api/schema/PipelineTemplate.html
+For more information and examples for writing pipelines, see the "pipeline template reference":{{site.baseurl}}/api/methods/pipeline_templates.html