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BioGrids Environment

The BioGrids environment manages bioinformatics software, handles version selection, resolves dependencies, and provides consistent interfaces for research workflows.

Key Components

Environment Variables

  • PATH management: Adds software directories automatically
  • Library paths: Configures LD_LIBRARY_PATH and dependencies
  • Version control: Manages active software versions

Shell Integration

  • biogrids.shrc: Main configuration for bash/zsh
  • biogrids.cshrc: Configuration for tcsh/csh
  • Module compatibility: Works with existing module systems

Software Capsules

  • Isolated environments: Software runs in controlled environments
  • Dependency resolution: Handles complex dependencies automatically
  • Version isolation: Multiple versions coexist without conflicts

Using the Environment

Activation

# Load BioGrids environment
source /programs/biogrids.shrc

# Use software directly
blast --version
samtools --help
python script.py

Configuration

Create ~/.biogrids.conf for personal settings: 

# Software versions
PYTHON_X=3.9.7
R_X=4.2.1
BLAST_X=2.12.0

# Environment variables
TMPDIR=/local/scratch
OMP_NUM_THREADS=8

Shell Integration

Add to your shell profile for automatic loading: 

# Bash/Zsh
echo 'source /programs/biogrids.shrc' >> ~/.bashrc

# Tcsh
echo 'source /programs/biogrids.cshrc' >> ~/.cshrc

Management Commands

Environment Operations

# Check environment status
biogrids-info --environment

# List available software
biogrids-info --list

# Get software information
biogrids-info blast

Version Management

# Set version for current session
export BLAST_X=2.11.0

# Check version precedence
biogrids-info blast --precedence

Site Administration

Administrators can configure site-wide defaults in /programs/local/conf/site.conf:

# Site-wide versions
PYTHON_X=3.9.7
R_X=4.2.1

# Site environment
SCRATCH_DIR=/local/scratch
LICENSE_SERVER=license.university.edu

Troubleshooting

Common Issues

  • Software not found: Ensure environment is sourced
  • Version conflicts: Check biogrids-info --precedence
  • Environment corruption: Run biogrids-reset --full

Getting Help