Configuration

Configuration Overview

Bio_pype uses a flexible configuration system that allows you to: - Customize module locations - Set system-specific parameters - Define execution environments - Manage resource limits

Module Paths

By default, Bio_pype modules (snippets, pipelines, profiles, and queues) are installed in Python’s site-packages directory. However, you can customize these locations to: - Make modules easier to edit and maintain - Switch between different module sets (e.g., stable vs. development) - Share modules across users or projects

Configuration Methods

1. Local Configuration File

The primary configuration file is located at ~/.bio_pype/config. Example:

PYPE_TMP=/tmp
PYPE_LOGDIR=/tmp/logs
PYPE_SNIPPETS=~/bio_pype/snippets
PYPE_PIPELINES=~/bio_pype/pipelines

2. Environment Variables

Environment variables override settings in the configuration file:

export PYPE_SNIPPETS=/custom/path/snippets
export PYPE_MEM="32GB"

Environment Configuration

The current module path is set to:

$ echo $PYPE_MODULES
test/data

Configuration Variables

Variable	Description
PYPE_MODULES	Base path for all module types (overrides individual module paths)
PYPE_SNIPPETS	Path to snippet modules
PYPE_PROFILES	Path to profile configurations
PYPE_PIPELINES	Path to pipeline definitions
PYPE_QUEUES	Path to queue system adapters
PYPE_REPOS	Path to repository configuration file
PYPE_NCPU	Maximum CPUs for parallel local execution
PYPE_MEM	Maximum memory for local execution
PYPE_TMP	Temporary directory (available as %(pype_tmp)s)
PYPE_LOGDIR	Log file directory (default: ~/.bio_pype/logs)
PYPE_DOCKER	Container runtime path (docker/singularity/udocker)
PYPE_SINGULARITY_CACHE	Singularity image cache directory