# Bio-MCP Configuration File
# This file allows you to configure tool execution preferences for HPC/cluster environments
# Global execution mode settings
execution:
# Force a specific execution mode for all tools
# Options: native, module, lmod, singularity, docker
# Leave empty to use automatic detection
force_mode: null
# Preferred execution modes in order of preference
# The system will try these modes in order until one works
preferred_modes:
- native # Tool available in PATH
- module # Tool available via Environment Modules
- lmod # Tool available via Lmod
- singularity # Tool available via Singularity container
- docker # Tool available via Docker container
# Module system settings
modules:
# Additional paths to search for modules
search_paths: []
# Tool-specific module names
tool_modules:
blast: ["blast", "blast+", "ncbi-blast+"]
samtools: ["samtools", "SAMtools"]
bwa: ["bwa", "BWA"]
bedtools: ["bedtools", "BEDTools"]
fastqc: ["fastqc", "FastQC"]
seqkit: ["seqkit", "SeqKit"]
bcftools: ["bcftools", "BCFtools"]
interpro: ["interproscan", "InterProScan"]
# Container settings
containers:
# Singularity settings
singularity:
# Path to directory containing Singularity images
image_path: null
# Custom image names
images:
blast: "biocontainers/blast:2.15.0"
samtools: "biocontainers/samtools:1.19.2"
bwa: "biocontainers/bwa:0.7.17"
bedtools: "biocontainers/bedtools:2.31.1"
fastqc: "quay.io/biocontainers/fastqc:0.12.1"
seqkit: "biocontainers/seqkit:2.8.1"
bcftools: "biocontainers/bcftools:1.19"
interpro: "biocontainers/interproscan:5.63_95.0"
# Docker settings
docker:
# Docker image prefix/registry
registry: "biocontainers"
# Custom image names
images:
blast: "biocontainers/blast:2.15.0"
samtools: "biocontainers/samtools:1.19.2"
bwa: "biocontainers/bwa:0.7.17"
bedtools: "biocontainers/bedtools:2.31.1"
fastqc: "quay.io/biocontainers/fastqc:0.12.1"
seqkit: "biocontainers/seqkit:2.8.1"
bcftools: "biocontainers/bcftools:1.19"
interpro: "biocontainers/interproscan:5.63_95.0"
# Performance settings
performance:
# Maximum file size for processing (in bytes)
max_file_size: 100000000 # 100MB
# Command timeout (in seconds)
timeout: 300 # 5 minutes
# Temporary directory for processing
temp_dir: null # Uses system default
# Logging settings
logging:
level: INFO
log_execution_commands: true
log_tool_detection: true
# Tool-specific overrides
# You can override settings for specific tools
tool_overrides:
blast:
# Force BLAST to use modules if available
execution_mode: module
timeout: 600 # 10 minutes for longer BLAST jobs
fastqc:
# FastQC can handle larger files
max_file_size: 10000000000 # 10GB
timeout: 1800 # 30 minutes
interpro:
# InterProScan typically needs more time
timeout: 3600 # 1 hour
# Environment variables
# These will be set when executing tools
environment:
# Common bioinformatics environment variables
NCBI_DATA_PATH: null
BLAST_DB_PATH: null
INTERPRO_DATA_PATH: null
