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Site Installation

A BioGrids site installation provides the complete software collection for Linux and/or macOS environments. This installation type is ideal for laboratories, departments, or institutions that need to provide BioGrids software to multiple users.

What is a Site Installation?

A site installation includes:

  • Complete Software Collection: Access to 500+ bioinformatics and computational biology applications
  • Automatic Updates: Monthly software updates and bug fixes delivered automatically
  • Multi-user Support: Shared installation accessible by multiple users
  • Network Storage Compatibility: Works with shared network file systems
  • Centralized Management: Single installation point for entire research groups

Benefits

One of the primary benefits of a BioGrids software installation is that it is a curated and actively managed software collection. New titles are added, obsolete versions are removed, and updates can happen automatically. That makes new software and bug fixes only an email request away (help@biogrids.org) without required system administration.

Installation Requirements

System Requirements

  • Linux: RHEL 7+, CentOS 7+, Ubuntu 18.04+, or compatible distributions
  • macOS: macOS 10.14 (Mojave) or later
  • Storage: Minimum 500GB available disk space (1TB+ recommended)
  • Memory: 8GB RAM minimum (16GB+ recommended for large workloads)
  • Network: Reliable internet connection for updates and downloads

Administrative Access

Site installations require: - Root or sudo access for initial installation - Ability to configure shared file system permissions - Network access for software updates and downloads

Installation Process

1. Request Site Installation

Contact the BioGrids team at help@biogrids.org to request a site installation. Include:

  • Institution/organization name
  • Expected number of users
  • Preferred installation location and file system type
  • Operating system(s) required (Linux/macOS)

2. Download Installation Manager

Once approved, you'll receive access to download the BioGrids Installation Manager specifically configured for site installations.

3. Initial Setup

Run the installation manager with administrative privileges:

sudo ./biogrids-install-manager --site-install

4. Configuration

The installation manager will guide you through: - Software collection selection - Installation location configuration
- User access permissions - Update schedule preferences

5. User Environment Setup

After installation, users can access BioGrids software by sourcing the environment:

source /programs/biogrids.shrc

Post-Installation Management

Automatic Updates

Site installations can be configured for automatic monthly updates. The system will: - Download new software versions - Remove deprecated packages - Apply security patches - Maintain software compatibility

Manual Management

Administrators can also manage updates manually using the BioGrids CLI administration tools:

biogrids-admin update
biogrids-admin list-available
biogrids-admin install <package>

User Management

Adding Users

Users need BioGrids consortium membership to access the software. Each user should:

  1. Register for a BioGrids account at biogrids.org
  2. Have their PI verify consortium membership
  3. Be added to the local system with appropriate file permissions

Access Control

Site installations support various access control methods: - LDAP/Active Directory integration - Local user groups - File system permissions - License server integration (where applicable)

Troubleshooting

Common Issues

Permission Errors - Verify users have read access to installation directory - Check that shared file system is properly mounted - Ensure environment variables are set correctly

Update Failures - Verify internet connectivity - Check disk space availability - Confirm administrative credentials are valid

Software Not Found - Verify BioGrids environment is properly sourced - Check software package is included in installation - Confirm software versions are compatible

Getting Help

For installation assistance: - Email: help@biogrids.org - Include system information and error messages - Provide installation logs when requesting support

Migration and Backup

Backup Recommendations

  • Backup installation configuration files
  • Document custom environment modifications
  • Maintain user account and permission records
  • Store installation logs and update history

Migration Between Systems

When migrating to new hardware: 1. Backup existing installation configuration 2. Install BioGrids on new system 3. Copy custom configurations and modifications 4. Test user access and software functionality 5. Update user environment scripts if needed

License Management

Some BioGrids software requires commercial licenses: - Configure license servers before installation - Ensure network access to license servers - Monitor license usage and compliance - Coordinate license renewals with vendors

Contact the BioGrids team for guidance on specific license requirements and configuration.