Albany

Version 2.0.1

LimsETL is a bioinformatics data extraction and processing pipeline that interfaces with IGO LIMS (Laboratory Information Management System) to retrieve genomic project metadata and generate standardized project files for downstream analysis pipelines.

Features

• Extract project metadata from IGO LIMS via REST API
• Generate pipeline-specific project files for variant calling, RNA-seq, and ChIP-seq
• Support for multiple sequencing zones (JUNO, IRIS) with dynamic path handling
• Automated sample-to-FASTQ mapping with comprehensive metadata
• Request merging capabilities for multi-request projects

Installation

Prerequisites

• Python 3.x
• R (for pipeline project generation)
• Access to IGO LIMS system

Setup

1. Clone repository
2. Install Python dependencies:

   pip3 install -r requirements.txt

3. Configure LIMS credentials:

   cp conf.py.tmpl conf.py

   Edit conf.py and set:

   self.LIMS_USERNAME="your_username"
   self.LIMS_PASSWORD="your_password"

Usage

Extract Project Data

python3 getProjectFiles.py <PROJECT_NUMBER>

Generates three output files:

• Proj_<ID>_metadata.yaml: Project-level metadata
• Proj_<ID>_sample_mapping.txt: Sample-to-file mappings
• Proj_<ID>_metadata_samples.csv: Detailed sample metadata

Key Features

• Environment zone detection for FASTQ path resolution
• Caching via cachier library for API performance
• Robust null value handling in metadata parsing
• Primary IGO ID validation to prevent duplicates

Testing

cd UnitTests
./doUnitTest01.sh