README.md

In legenepi/exceed-pipelines: Reusable pipelines for the EXCEED study

exceed.pipelines

The pipeline interface is designed to allow writing and sharing of reusable code and minimizing the duplication of effort.

Introduction

For an introduction to pipelines, please review the following:

• vignette on pipelines in exceedapi package documentation.
• chapter 4 on pipelines in exceedapi-tutorial.

Getting started

By default, exceedapi will search for reusable steps in the current environment or in the main branch in legenepi/exceed-pipelines repository on github. No configuration is necessary but if you're loading steps from the GitHub repo then it's recommended that you create a GitHub Personal Access Token (PAT) with repo scope, and set it using gitcreds::gitcreds_set(). For more information on using GitHub Personal Access Token (PAT) in R, follow the guide at Happy Git

Pipelines can also loaded from a local directory or from any other github repo. For example, if you want to load steps from the main branch in a repo named skyfall under the account bond, you would create a .yaml config file with the following:

pipeline:
  search:
  - bond/skyfall@main
  - legenepi/exceed-pipelines@main:R

This would add bond/skyfall repo as the first place where exceedapi would look for steps, followed by the default legenepi/exceed-pipelines

You can specify the exact version to load from GitHub using the standard GitHub syntax for referencing branches and tags. For example, to load a specific version from the default repo, you can create a config file with the following:

pipeline:
  search:
  - legenepi/exceed-pipelines@v0.4.0:R

You also need to decide whether you want this to be a per-project configuration file or a global one.

• For per-project files, create an exceedapi.yaml in the top-level directory of your project.

• For global configuration files create .exceedapi.yaml in your home directory.

In most cases, it's recommended to create a per-project configuration files, kept in separate directories.

NOTE: the name of configuration file is different if it's in the home directory and must start with a dot .

Installing the package

Installing the package is not required if you just want to load pipeline steps from GitHub directly. You could, however, install exceed.pipelines as a package but keep in mind you'd have to update it whenever new functionality is added.

You can install the latest version of exceed.pipelines package from the development server:

install.packages("https://dev.exceed.le.ac.uk/exceed-pipelines/dist/exceed.pipelines.tar.gz")

All previous versions of the package are archived here.

legenepi/exceed-pipelines documentation built on Oct. 22, 2024, 7:48 p.m.