P PluMA Plugin-Based Microbiome Analysis

Getting Started

Install, build, and run your first pipeline

PluMA's core is small and its plugin model keeps installations lightweight — you only pull in the stages your pipeline actually needs.

Step 1

Clone the repository

Clone the PluMA core from GitHub. The build system uses SCons with a lightweight Python configuration layer (build_config.py, build_support.py).
```
git clone https://github.com/FIUBioRG/PluMA.git
cd PluMA
```
Step 2

Build PluMA

Install the Python requirements, then build with SCons. A Dockerfile is provided if you prefer a containerized build.
```
pip install -r requirements.txt
scons
```
Step 3

Add plugins

Drop plugins into the plugins/ directory, or point PLUMA_PLUGIN_PATH at a different location. Browse the plugin catalog to find stages for your workflow.
```
export PLUMA_PLUGIN_PATH=/path/to/plugins
```
Step 4

Run a pipeline

A pipeline is a configuration file that lists stages in order. Example pipelines live in pipelines/ inside the repo.
```
./pluma pipelines/example.pipeline
```