Pipeline template development » History » Version 3

Bryan Cosca, 04/19/2016 08:18 PM

1 1 Bryan Cosca
h1. Pipeline template development
2 1 Bryan Cosca
3 2 Bryan Cosca
This wiki will describe how to write a pipeline template. Some documentation for writing a pipeline template using run-command is available on "doc.arvados.org":http://doc.arvados.org/user/tutorials/running-external-program.html
4 2 Bryan Cosca
5 2 Bryan Cosca
6 2 Bryan Cosca
"components": {
7 2 Bryan Cosca
 "JobName": {
8 2 Bryan Cosca
  "script": "JobScript",
9 2 Bryan Cosca
  "script_version": "master",
10 2 Bryan Cosca
  "repository": "yourname/yourname",
11 2 Bryan Cosca
  "script_parameters": {
12 2 Bryan Cosca
   "CollectionOne": {
13 2 Bryan Cosca
    "required": true,
14 2 Bryan Cosca
    "dataclass": "Collection"
15 2 Bryan Cosca
16 2 Bryan Cosca
17 2 Bryan Cosca
    "required": true,
18 2 Bryan Cosca
    "dataclass": "text",
19 2 Bryan Cosca
    "default": "ParameterOneString"
20 2 Bryan Cosca
21 2 Bryan Cosca
22 2 Bryan Cosca
  "runtime_constraints": {
23 2 Bryan Cosca
   "docker_image": "bcosc/arv-base-java",
24 2 Bryan Cosca
   "arvados_sdk_version": "master"
25 2 Bryan Cosca
26 2 Bryan Cosca
27 2 Bryan Cosca
28 2 Bryan Cosca
29 2 Bryan Cosca
30 1 Bryan Cosca
How to wrap a git repository containing a crunch script and a docker image into a component
31 1 Bryan Cosca
Link to "Git Strategy for Pipeline Development" wiki page
32 1 Bryan Cosca
33 2 Bryan Cosca
h3. Writing script_parameters
34 1 Bryan Cosca
35 2 Bryan Cosca
"Script_parameters":http://doc.arvados.org/api/schema/PipelineTemplate.html are inputs that can be called in your crunch script. Each script parameter can have any dataclass: Collection, File, number, text. Collection passes in the pdh string (ex. 39c6f22d40001074f4200a72559ae7eb+5745), File passes in a file path in a collection (ex. 39c6f22d40001074f4200a72559ae7eb+5745/foo.txt), number passes in any integer, and text passes in any string.
36 1 Bryan Cosca
37 2 Bryan Cosca
The default parameter is useful for using a collection you know will most likely be used, so the user does not have to input it manually. For example, a reference genome collection that will be used throughout the entire pipeline.
38 2 Bryan Cosca
39 2 Bryan Cosca
The title and description parameters are useful for showing what the script parameter is doing, but is not necessary.
40 2 Bryan Cosca
41 2 Bryan Cosca
h3. Writing runtime_constraints
42 2 Bryan Cosca
43 2 Bryan Cosca
"Runtime_constraints":http://doc.arvados.org/api/schema/Job.html are inputs in your job that help choose node parameters that your pipeline will run on. Optimizing these parameters can be found in the "Pipeline_Optimization wiki.":https://dev.arvados.org/projects/arvados/wiki/Pipeline_Optimization
44 2 Bryan Cosca
45 3 Bryan Cosca
One notable runtime constraint is the arvados_sdk_version. Currently, we do not suggest you use this for production, as it can break pipeline reproducibility. Feel free to use this while developing a pipeline template, as it can be useful to get the specific sdk version you want before downloading it straight into the docker image.
46 3 Bryan Cosca
47 3 Bryan Cosca
Another runtime constraint is docker_image. It is suggested that while developing you use the latest version of the image, which you can specify by using the name of the image. When in production, you should use the portable data hash of the image you specifically want to use to avoid problems when accidentally changing the image or other conflicts.
48 3 Bryan Cosca
49 3 Bryan Cosca
Using min_nodes will spin up as many nodes as you've specified. Be warned that you can allocate your entire cluster to your job, so use this with caution.
50 3 Bryan Cosca
51 3 Bryan Cosca
The max_tasks_per_node parameter will allow you to allocate more computations on your node. By default, this is 1. If you are under utilizing your nodes, you can try to increase this number. Keep in mind that the total CPU/RAM/space usage of your tasks should fit on your node. It's very easy to overestimate the compute power of your tasks. Using something like "crunchstat-summary":https://dev.arvados.org/projects/arvados/wiki/Pipeline_Optimization should help bridge this gap.