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Site Administration Guide

This guide is intended for system administrators managing institutional BioGrids installations, including multi-user systems and high-performance computing (HPC) clusters.

Initial Setup & Installation

1. Request a Site Installation

Contact the BioGrids team at help@biogrids.org to request a site key. Provide your institution name and the expected number of users.

2. Create a Service Account

We recommend creating a dedicated biogrids user to manage the installation. 

sudo adduser biogrids
sudo su - biogrids

3. Activate the Site

Download the CLI tool and activate your site: 

./biogrids-cli activate-site --target /data/biogrids

BioGrids requires a root-level symlink. * Linux: sudo ln -sf /data/biogrids /programs * macOS: Use /etc/synthetic.conf (requires reboot).

Software Management

Common Admin Commands

Manage the entire collection using the admin subcommand:

  • Install All Software: biogrids-cli admin --all-versions
  • Check for Updates: biogrids-cli updates
  • Remove Obsolete Versions: biogrids-cli clean
  • Parallel Processing: Add -j <threads> (e.g., -j 8) to speed up operations.

Automated Updates

Configure automatic updates via cron to keep your site synchronized with the latest releases: 

biogrids-cli crontab --all-versions -j 4

Configuration & Overrides

Administrators can set site-wide defaults that apply to all users.

Site-Wide Overrides

Create or edit /programs/admin/overrides.conf to pin specific versions: 

[global]
PYTHON_X=3.9.7
R_X=4.2.1

[genomics]
BLAST_X=2.12.0
SAMTOOLS_X=1.15

Collection Management

You can group software into custom collections for specific labs or projects in /programs/admin/collections.conf.

License Management

For commercial software (e.g., MATLAB, Schrodinger), configure license servers in /programs/admin/licenses.conf: 

[matlab]
license_type = "server"
license_server = "license.university.edu"
license_port = "27000"

Multi-User Management

Access Control

  • User Groups: Add users to a biogrids-users group to manage read/execute permissions.
  • Restricting Software: Use biogrids-cli admin restrict-access <software> --group <group> to limit access to licensed tools.

Environment Setup for Users

Add the following to the system-wide shell profiles (e.g., /etc/bash.bashrc): 

source /programs/biogrids.shrc

Backup & Migration

  • Metadata Backup: biogrids-cli save > site-config.json
  • Full Mirror: Use rsync -av /programs/ backup-server:/path/
  • Migration: On a new server, use biogrids-cli reactivate site-config.json.

Support

For complex institutional deployments, cluster architecture planning, or performance tuning, contact our technical team:

help@biogrids.org