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Personal Installation

Personal installations of BioGrids are ideal for individual researchers who want to install specific software packages on their personal workstation or laptop. This installation type offers flexibility and efficiency by allowing you to select only the software you need.

What is a Personal Installation?

A personal installation provides:

  • Selective Software Installation: Choose only the applications you need
  • Smaller Disk Footprint: Reduced storage requirements compared to full site installations
  • User-Controlled Updates: Install updates when convenient for your workflow
  • Cross-Platform Support: Available for both Linux and macOS
  • Easy Management: Simple installation and maintenance process

Installation Methods

BioGrids offers two personal installation methods:

The graphical installation manager provides an intuitive interface for software selection and management.

Features: - User-friendly graphical interface - Browse available software by category - Read software descriptions and documentation - Install/uninstall packages with a single click - Automatic dependency resolution - Update notifications

Best for: Users who prefer visual interfaces and occasional software management.

2. CLI Installation Manager (Advanced)

The command-line installation manager offers powerful automation and scripting capabilities.

Features: - Command-line driven package management - Scriptable installation and updates - Batch operations for multiple packages - Integration with system automation - Detailed logging and reporting

Best for: Advanced users, system administrators, and automated workflows.

System Requirements

Minimum Requirements

  • Linux: RHEL 7+, CentOS 7+, Ubuntu 18.04+, or compatible distributions
  • macOS: macOS 10.14 (Mojave) or later
  • Storage: 50GB available disk space (varies by software selection)
  • Memory: 4GB RAM minimum
  • Network: Internet connection for downloads and updates
  • Storage: 200GB+ available space for comprehensive software selection
  • Memory: 8GB+ RAM for optimal performance
  • Network: Broadband connection for faster downloads

Installation Process

Step 1: Membership and Account Setup

  1. Join BioGrids Consortium: Visit biogrids.org/join to apply for membership
  2. Register Account: Create a BioGrids account with institutional email address
  3. PI Verification: Have your Principal Investigator verify your membership status

Step 2: Download Installation Manager

  1. Log into your BioGrids account at biogrids.org
  2. Navigate to the Downloads section
  3. Download the appropriate installation manager for your platform:
  4. Linux: biogrids-install-manager-linux.tar.gz
  5. macOS: biogrids-install-manager-macos.dmg

Step 3: Initial Setup

Linux Installation

# Extract the installation manager
tar -xzf biogrids-install-manager-linux.tar.gz
cd biogrids-install-manager

# Run the installer
./install.sh

macOS Installation

  1. Mount the DMG file by double-clicking
  2. Drag BioGrids Installation Manager to Applications folder
  3. Launch the application from Applications or Launchpad

Step 4: Software Selection and Installation

GUI Method

  1. Launch the BioGrids Installation Manager
  2. Sign in with your BioGrids account credentials
  3. Browse available software categories
  4. Select desired applications and click "Install"
  5. Monitor installation progress and completion

CLI Method

# List available software
biogrids-cli list-available

# Install specific software
biogrids-cli install <package-name>

# Install multiple packages
biogrids-cli install package1 package2 package3

# Update all installed software
biogrids-cli update-all

Using BioGrids Software

After installation, activate the BioGrids environment:

# Source the BioGrids environment
source ~/.biogrids/biogrids.shrc

# Verify installation
biogrids-cli list-installed

# Run BioGrids software
<software-name> --version

Managing Your Installation

Adding New Software

GUI Method: - Open Installation Manager - Browse or search for new software - Click "Install" for desired packages

CLI Method: 

biogrids-cli search <software-name>
biogrids-cli install <software-name>

Updating Software

Automatic Updates (GUI): - Installation Manager will notify you of available updates - Review and approve updates through the interface

Manual Updates (CLI): 

# Check for updates
biogrids-cli check-updates

# Update specific software
biogrids-cli update <package-name>

# Update all software
biogrids-cli update-all

Removing Software

GUI Method: - Open Installation Manager - Go to "Installed Software" tab - Click "Uninstall" for unwanted packages

CLI Method: 

biogrids-cli remove <package-name>

Configuration Options

Installation Directory

By default, BioGrids installs to: - Linux: ~/.biogrids/ - macOS: ~/Library/BioGrids/

To specify a custom location: 

biogrids-cli config set install-path /custom/path/biogrids

Environment Integration

Add BioGrids to your shell profile for automatic activation:

# For bash users
echo 'source ~/.biogrids/biogrids.shrc' >> ~/.bashrc

# For zsh users (macOS default)
echo 'source ~/.biogrids/biogrids.shrc' >> ~/.zshrc

Proxy Configuration

For installations behind corporate firewalls:

biogrids-cli config set proxy-server http://proxy.example.com:8080
biogrids-cli config set proxy-username your_username

Troubleshooting

Common Issues

Installation Fails with Permission Errors: - Ensure sufficient disk space in installation directory - Check that installation directory is writable - Verify network connectivity to BioGrids servers

Software Not Found After Installation: - Verify BioGrids environment is properly sourced - Check installation completed successfully - Restart terminal session

Update Failures: - Check internet connectivity - Verify BioGrids account credentials are valid - Ensure sufficient disk space for updates

Getting Help

For installation assistance: - Email: help@biogrids.org - Documentation: Check installation logs in ~/.biogrids/logs/ - Community: Join the BioGrids mailing list

Log Files

Installation and error logs are stored in: - Linux: ~/.biogrids/logs/ - macOS: ~/Library/BioGrids/logs/

Include relevant log excerpts when requesting support.

Advanced Configuration

Multiple Environments

Create separate BioGrids environments for different projects:

# Create project-specific environment
biogrids-cli create-env project1 --path ~/biogrids-project1

# Activate specific environment
source ~/biogrids-project1/biogrids.shrc

Integration with Version Control

Track your BioGrids configuration with version control:

# Export installed package list
biogrids-cli export-config > biogrids-packages.txt

# Import configuration on new system
biogrids-cli import-config biogrids-packages.txt

Performance Optimization

Optimize BioGrids performance for your workflow:

# Enable parallel downloads
biogrids-cli config set parallel-downloads 4

# Configure cache settings
biogrids-cli config set cache-size 10GB