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Using BioGrids

This guide covers everything you need to know about using the BioGrids software collection, from initial setup to advanced version management.

Getting Started

1. Initialize the Environment

The software is installed at /programs. Before running any tools, you must source the initialization script for your shell.

source /programs/biogrids.shrc

source /programs/biogrids.cshrc

2. Automatic Loading

To load BioGrids automatically in every new terminal session, add the command above to your shell configuration file (e.g., ~/.bashrc, ~/.zshrc, or ~/.tcshrc).

3. Verify Activation

Once initialized, you should see the BioGrids welcome message. You can also verify the root path: 

echo $BIOGRIDS_ROOT
# Should return /programs

Working with Software

### :material-magnify: Looking for a specific tool? BioGrids includes over 800+ applications. You can search the full collection using the CLI: 
biogrids-cli search <name>
Or browse the [**Online Software Catalog**](https://biogrids.org/software/).

Exploring the Catalog

BioGrids provides hundreds of pre-compiled applications.

  • List All Available Software: 
    # Linux
cat /programs/x86_64-linux/biogrids_x86_64-linux
# macOS
cat /programs/i386-mac/biogrids_i386-mac
  • Get Software Details: 
    biogrids-info -l samtools

Common Tools

Most users start with these essential packages: * Sequence Analysis: blast+, samtools, bwa, bowtie2 * Genomics: gatk, star, bedtools * Languages: python, r, perl

Isolated Environments (Capsules)

BioGrids uses a Capsule system to isolate applications. This prevents dependency conflicts and ensures that running one tool doesn't interfere with another. * No Conflicts: Multiple versions of the same tool can coexist. * Reproducibility: The environment is identical across different machines. * Performance: Optimized binaries run natively with minimal overhead.

Managing Versions

By default, BioGrids uses the most recent stable version of each application. You can easily override this for specific projects.

Temporary (Session-only)

Use environment variables to switch versions for your current terminal session. 

# Linux
export SAMTOOLS_X=1.12
# macOS
export SAMTOOLS_M=1.12

Persistent (Global)

Create or edit ~/.biogrids.conf to set your preferred defaults across all sessions: 

# Example ~/.biogrids.conf
PYTHON_X=3.9.7
R_X=4.2.1
BLAST_X=2.12.0

Selection Priority

BioGrids resolves versions in this order (highest to lowest): 1. Environment Variables (Current shell) 2. User Configuration (~/.biogrids.conf) 3. Site Configuration (Set by your local admin) 4. BioGrids Defaults (Standard stable version)

Common Workflows

Sequence Analysis

source /programs/biogrids.shrc
bwa mem reference.fa reads_1.fq reads_2.fq > alignment.sam
samtools view -bS alignment.sam > alignment.bam

Data Analysis

source /programs/biogrids.shrc
R --vanilla < analysis_script.R
python data_analysis.py

Troubleshooting

  • Command not found: Ensure you have run source /programs/biogrids.shrc.
  • Wrong version: Use biogrids-info <tool> --precedence to see why a specific version was chosen.
  • Environment corruption: Run biogrids-reset --full to restore default settings.

Need help? Contact our experts at help@biogrids.org.