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BioGrids Installation Manager GUI

The BioGrids graphical installation manager provides an intuitive, user-friendly interface for installing and managing bioinformatics software. This guide covers installation and usage of the GUI version.

JV: Sep 8 FIX ALL IMAGES

Prerequisites

System Requirements

  • Supported platforms: Linux and macOS
  • Installation privileges: Administrator access required for initial setup only
  • BioGrids account: Valid consortium membership and user account required

BioGrids Account Setup

  1. Join BioGrids Consortium: Apply at biogrids.org/join
  2. Register account: Create account at biogrids.org/registration using institutional email
  3. PI verification: Have your Principal Investigator verify your consortium membership

All versions of the installation manager are available for download here.

Installation Directory and Permissions

The BioGrids installation manager installs software to /opt/biogrids by default. A symlink from /programs to the installation directory is required.

Important: Administrator privileges are only needed for: - Creating the /opt/biogrids installation directory - Creating the required /programs symlink - Normal software usage does not require admin privileges

The Installation Manager uses sudo for privileged installation tasks and should be run from an account with sudo privileges for initial setup.

Platform-Specific Setup

macOS Configuration

On macOS Catalina and later, a /etc/synthetic.conf file is required to create the root-level /programs symlink. The GUI installation manager handles this automatically, but a system reboot is required after initial activation.

Linux Configuration

On Linux systems, the installation manager can create the necessary directories and symlinks automatically with sudo privileges.

Getting Started

Download and Launch

  1. Download the GUI installation manager from the downloads page
  2. Linux: Extract and run the executable
  3. macOS: Mount the DMG and drag to Applications folder

First-Time Activation

The first step is to activate your BioGrids account. This is a one-time process per installation.

Activation Screen

  1. Enter credentials: Provide your BioGrids site, username, and activation key
  2. Click "Activate": Begin the activation process
  3. Confirm permissions: Allow the installer to create necessary directories

Permission Dialogs

On macOS, you'll see permission requests:

macOS Permissions

This permission is only needed to create the /opt/biogrids directory.

Synthetic.conf Setup

The /etc/synthetic.conf file is required for the /programs symlink on macOS. A reboot is required after this setup.

Using the GUI Installation Manager

Home Screen

GUI Home Screen

The home screen features: - New and Updated Software: Recently added or updated packages - BioGrids News: Announcements, webinars, and community updates
- Navigation Panel: Six main sections for managing your installation

Main Interface Sections

1. Installed Software

Installed Pane

View currently installed software packages. Initially, only the BioGrids Installer base system is present.

Software Details

Click any software title to view detailed information including: - Software description and version - Installation status and dependencies - Documentation links and usage notes

2. Available Programs

Programs Pane

Browse all available bioinformatics software. This pane allows you to: - Search for specific software packages - Filter by category or collection - Add/Remove software (operations are queued for execution) - Upgrade to newer versions

Added to Queue

Software operations are added to the task queue for batch processing.

3. Task Management

Task List

All installation, removal, and upgrade operations are managed through the task list: - Review pending operations before execution - Remove tasks if you change your mind - Execute all tasks when ready

Running Tasks

Tasks run in parallel with progress indicators. Multiple downloads and installations can occur simultaneously for efficiency.

Software Operations

Installing Software

  1. Navigate to the "Programs" pane
  2. Find desired software using search or browsing
  3. Click the blue "Install" text next to the software name
  4. Review the task in the task list
  5. Execute tasks to begin installation

Upgrading Software

  1. Check for available updates in the "Programs" pane
  2. Click the green "Upgrade" text for software with updates
  3. Execute upgrade tasks to install newer versions

Removing Software

  1. Navigate to the "Installed" pane
  2. Click the red "Remove" text next to unwanted software
  3. Confirm removal in the task list
  4. Execute removal tasks

Advanced Features

Collections and Categories

BioGrids organizes software into collections like: - Genomics: DNA/RNA sequencing and analysis tools - Proteomics: Protein analysis and mass spectrometry - Structural Biology: Molecular visualization and modeling - Statistics: R, Python, and statistical analysis packages

Proxy Configuration

For networks requiring HTTP proxies: 1. Open Preferences dialog 2. Configure proxy settings (server, port, authentication) 3. Enable/disable proxy as needed (useful for mobile users)

Documentation and Support

  • Docs Pane: Access to BioGrids documentation wiki
  • Contact Pane: Bug reporting and support contact information
  • Built-in Help: Context-sensitive help throughout the interface

Troubleshooting

Common Issues

"Cannot verify developer" (macOS) - Cancel the dialog and run: xattr -d com.apple.quarantine BioGrids-Installer.app - Alternative: Download using curl instead of web browser

Permission Denied Errors - Ensure you have sudo privileges on the system - Check that installation directory is writable - Verify network connectivity to BioGrids servers

Software Not Appearing - Refresh the programs list (restart the GUI) - Verify your BioGrids account has access to the desired software - Check that you're viewing the correct platform (Linux/macOS)

Installation Failures - Check network connectivity and firewall settings - Ensure sufficient disk space in installation directory - Review error logs in the GUI for specific failure reasons

Network Configuration

The GUI installation manager requires outbound internet access: - HTTPS (port 443): Primary download protocol - HTTP (port 80): Fallback for some repositories - Configure proxy settings if required by your network

Getting Help

For GUI-specific issues: - Email: help@biogrids.org - Include: Screenshots of any error messages - Provide: System information (OS version, BioGrids account details) - Attach: Log files from installation attempts

Video Tutorial

A video tutorial of the BioGrids Installation Manager demonstrates the complete installation and usage process.

Interoperability with CLI

The GUI and CLI installation managers are fully interchangeable: - Use GUI for initial setup and software browsing - Use CLI for scripting and automation - Both tools work with the same installation and configuration - Switch between interfaces as needed for different tasks

The GUI provides an excellent starting point for new users, while the CLI offers advanced features for experienced users and system administrators.