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User Manual

Once BioGrids is installed, follow this guide to set up your shell environment and start running applications.

1. Quick Start (Initialization)

To use any BioGrids software, you must first initialize the environment in your terminal session.

Manual Activation

Run the script appropriate for your shell:

source /programs/biogrids.shrc

source /programs/biogrids.cshrc

Automatic Loading

Add the activation command to your shell configuration file (e.g., ~/.bashrc or ~/.zshrc) to load BioGrids automatically every time you open a terminal.

Example for Bash: 

echo "source /programs/biogrids.shrc" >> ~/.bashrc

2. Working with Software

BioGrids uses a Capsule system to isolate applications, preventing dependency conflicts and ensuring reproducible results across different machines.

Finding Tools

Search the collection of 800+ applications using the CLI: 

biogrids-cli search <name>
Browse Online Software Catalog

Managing Versions

By default, BioGrids uses the most recent stable version. You can override this using environment variables.

  • Temporary (Current session): export SAMTOOLS_X=1.12
  • Persistent (Global): Add SAMTOOLS_X=1.12 to your ~/.biogrids.conf file.

3. Quick Reference (CLI)

Task Command
Search for a tool biogrids-cli search <name>
Install a tool biogrids-cli install <name>
List installed software biogrids-cli list --installed
Get Details on a package biogrids-info -l <name>
Check environment status biogrids-info --environment
Reset environment biogrids-reset --full

Support

For assistance with environment configuration, shell integration, or version management, contact our technical team:

help@biogrids.org