X-Git-Url: https://git.arvados.org/arvados.git/blobdiff_plain/26446197bb00d7f899673b7f9434e6bd622b8904..77f1129ec53edffb5ed5a859106675cf262977e8:/doc/user/tutorials/tutorial-firstscript.html.textile.liquid
diff --git a/doc/user/tutorials/tutorial-firstscript.html.textile.liquid b/doc/user/tutorials/tutorial-firstscript.html.textile.liquid
index a3b7e54edb..1269699a20 100644
--- a/doc/user/tutorials/tutorial-firstscript.html.textile.liquid
+++ b/doc/user/tutorials/tutorial-firstscript.html.textile.liquid
@@ -2,94 +2,94 @@
layout: default
navsection: userguide
navmenu: Tutorials
-title: "Writing a pipeline"
+title: "Writing a script"
...
-In this tutorial, we will write the "hash" script demonstrated in the first tutorial.
+This tutorial demonstrates how to write crunch script using the Arvados Python SDK. The Arvados SDK supports access to advanced features not available using the @run-command@ wrapper, such as scheduling parallel tasks across nodes.
-*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*
+{% include 'tutorial_expectations' %}
-This tutorial uses *@you@* to denote your username. Replace *@you@* with your user name in all the following examples.
+This tutorial uses @$USER@ to denote your username. Replace @$USER@ with your user name in all the following examples.
h2. Setting up Git
-As discussed in the previous tutorial, all Crunch scripts are managed through the @git@ revision control system.
-
-First, you should do some basic configuration for git (you only need to do this the first time):
+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.email $USER@example.com
~$ git config --global user.name "Your Name"
-~$ git config --global user.email you@example.com
git@git.{{ site.arvados_api_host }}:you.git
git@git.{{ site.arvados_api_host }}:$USER.git
+~$ git clone git@git.{{ site.arvados_api_host }}:you.git
-Cloning into 'you'...
~$ cd $HOME # (or wherever you want to install)
+~$ git clone git@git.{{ site.arvados_api_host }}:$USER.git
+Cloning into '$USER'...
$ man gittutorial
-or "click here to search Google for git tutorials":http://google.com/#q=git+tutorial
+or *"search Google for Git tutorials":http://google.com/#q=git+tutorial*.
{% include 'notebox_end' %}
h2. Creating a Crunch script
-Start by entering the *@you@* directory created by @git clone@. Next create a subdirectory called @crunch_scripts@ and change to that directory:
+Start by entering the @$USER@ directory created by @git clone@. Next create a subdirectory called @crunch_scripts@ and change to that directory:
~$ cd you
-~/you$ mkdir crunch_scripts
-~/you$ cd crunch_scripts
+~$ cd $USER
+~/$USER$ mkdir crunch_scripts
+~/$USER$ cd crunch_scripts
~/you/crunch_scripts$ nano hash.py
+notextile. ~/$USER/crunch_scripts$ nano hash.py
-Add the following code to compute the md5 hash of each file in a collection:
+Add the following code to compute the MD5 hash of each file in a collection:
~/you/crunch_scripts$ chmod +x hash.py
+notextile. ~/$USER/crunch_scripts$ chmod +x hash.py
{% include 'notebox_begin' %}
-The steps below describe how to execute the script after committing changes to git. To run a script locally for testing, please see "debugging a crunch script":{{site.baseurl}}/user/topics/tutorial-job-debug.html .
+The steps below describe how to execute the script after committing changes to Git. To run a script locally for testing, please see "debugging a crunch script":{{site.baseurl}}/user/topics/tutorial-job-debug.html.
{% include 'notebox_end' %}
-Next, add the file to @git@ staging. This tells @git@ that the file should be included on the next commit.
+Next, add the file to the staging area. This tells @git@ that the file should be included on the next commit.
-notextile. ~/you/crunch_scripts$ git add hash.py
+notextile. ~/$USER/crunch_scripts$ git add hash.py
-Next, commit your changes to git. All staged changes are recorded into the local @git@ repository:
+Next, commit your changes. All staged changes are recorded into the local git repository:
~/you/crunch_scripts$ git commit -m"my first script"
+~/$USER/crunch_scripts$ git commit -m"my first script"
[master (root-commit) 27fd88b] my first script
- 1 file changed, 33 insertions(+)
+ 1 file changed, 45 insertions(+)
create mode 100755 crunch_scripts/hash.py
~/you/crunch_scripts$ git push origin master
+~/$USER/crunch_scripts$ 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:you.git
+To git@git.qr1hi.arvadosapi.com:$USER.git
* [new branch] master -> master
~/you/crunch_scripts$ cd ~
+~/$USER/crunch_scripts$ cd ~
~$ cat >the_pipeline <<EOF
{
"name":"My first pipeline",
@@ -111,8 +111,12 @@ Next, create a file that contains the pipeline definition:
"dataclass": "Collection"
}
},
- "repository":"you",
- "script_version":"master"
+ "repository":"$USER",
+ "script_version":"master",
+ "output_is_persistent":true,
+ "runtime_constraints":{
+ "docker_image":"arvados/jobs"
+ }
}
}
}
@@ -120,22 +124,17 @@ EOF
~$ arv pipeline_template create --pipeline-template "$(cat the_pipeline)"