X-Git-Url: https://git.arvados.org/arvados.git/blobdiff_plain/715869b9a22e22ac68a7dbefa96f27150017f75d..2b5d9607892a48d32401ff59516e8d73234eee89:/doc/user/tutorials/running-external-program.html.textile.liquid
diff --git a/doc/user/tutorials/running-external-program.html.textile.liquid b/doc/user/tutorials/running-external-program.html.textile.liquid
index e286013247..56b71c05ee 100644
--- a/doc/user/tutorials/running-external-program.html.textile.liquid
+++ b/doc/user/tutorials/running-external-program.html.textile.liquid
@@ -1,67 +1,68 @@
---
layout: default
navsection: userguide
-navmenu: Tutorials
-title: "Running external programs"
-
+title: "Using Crunch to run external programs"
...
-h1. Running external programs
-
This tutorial demonstrates how to use Crunch to run an external program by writting a wrapper using the Python SDK.
-*This tutorial assumes that you are "logged into an Arvados VM instance":{{site.basedoc}}/user/getting_started/ssh-access.html#login, and have a "working environment.":{{site.basedoc}}/user/getting_started/check-environment.html*
+*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*
In this tutorial, you will use the external program @md5sum@ to compute hashes instead of the built-in Python library used in earlier tutorials.
Start by entering the @crunch_scripts@ directory of your git repository:
-$ cd you/crunch_scripts
+~$ cd you/crunch_scripts
-
-Next, using your favorite text editor, create a new file called @run-md5sum.py@ in the @crunch_scripts@ directory. Add the following code to use the @md5sum@ program to compute the hash of each file in a collection:
-{% include 'run_md5sum_py' %}
+Next, using @nano@ or your favorite Unix text editor, create a new file called @run-md5sum.py@ in the @crunch_scripts@ directory.
+
+notextile. ~/you/crunch_scripts$ nano run-md5sum.py
+
+Add the following code to use the @md5sum@ program to compute the hash of each file in a collection:
+
+ {% code 'run_md5sum_py' as python %}
Make the file executable:
-notextile. $ chmod +x run-md5sum.py
+notextile. ~/you/crunch_scripts$ chmod +x run-md5sum.py
-Next, add the file to @git@ staging, commit and push:
+Next, use @git@ to stage the file, commit, and push:
-$ git add run-md5sum.py
-$ git commit -m"run external md5sum program"
-$ git push origin master
+~/you/crunch_scripts$ git add run-md5sum.py
+~/you/crunch_scripts$ git commit -m"run external md5sum program"
+~/you/crunch_scripts$ git push origin master
-You should now be able to run your new script using Crunch, with "script" referring to our new "run-md5sum.py" script.
+You should now be able to run your new script using Crunch, with @"script"@ referring to our new @run-md5sum.py@ script.
-$ cat >the_job <<EOF
+~/you/crunch_scripts$ cat >~/the_pipeline <<EOF
{
- "script": "run-md5sum.py",
- "script_version": "you:master",
- "script_parameters":
- {
- "input": "c1bad4b39ca5a924e481008009d94e32+210"
- }
-}
-EOF
-$ arv -h job create --job "$(cat the_job)"
-{
- ...
- "uuid":"qr1hi-xxxxx-xxxxxxxxxxxxxxx"
- ...
-}
-$ arv -h job get --uuid qr1hi-xxxxx-xxxxxxxxxxxxxxx
-{
- ...
- "output":"4d164b1658c261b9afc6b479130016a3+54",
- ...
+ "name":"Run external md5sum program",
+ "components":{
+ "do_hash":{
+ "script":"run-md5sum.py",
+ "script_parameters":{
+ "input":{
+ "required": true,
+ "dataclass": "Collection"
+ }
+ },
+ "repository":"$USER",
+ "script_version":"master"
+ }
+ }
}
+EOF
+
~/you/crunch_scripts$ arv pipeline_template create --pipeline-template "$(cat ~/the_pipeline)"
+
+(Your shell should automatically fill in @$USER@ with your login name. The JSON that gets saved should have @"repository"@ pointed at your personal git repository.)
+
+Your new pipeline template will appear on the Workbench "Compute %(rarr)→% Pipeline templates":https://{{ site.arvados_workbench_host }}/pipeline_instances page. You can run the "pipeline using Workbench":tutorial-pipeline-workbench.html.