Skip to content

Installation Guide

This guide covers installation of Git DRS across different environments and target DRS servers.

Prerequisites

All installations require Git LFS to be installed first:

# macOS
brew install git-lfs

# Linux (download binary)
wget https://github.com/git-lfs/git-lfs/releases/download/v3.7.0/git-lfs-linux-amd64-v3.7.0.tar.gz
tar -xvf git-lfs-linux-amd64-v3.7.0.tar.gz
export PREFIX=$HOME
./git-lfs-v3.7.0/install.sh

# Configure LFS
git lfs install --skip-smudge

Local Installation (Gen3 Server)

Target Environment: Local development machine targeting Gen3 data commons (e.g., CALYPR)

Steps

  1. Install Git DRS 

    /bin/bash -c "$(curl -fsSL https://raw.githubusercontent.com/calypr/git-drs/refs/heads/main/install.sh)"

  2. Update PATH 

    # Add to ~/.bash_profile or ~/.zshrc
export PATH="$PATH:$HOME/.local/bin"
source ~/.bash_profile  # or source ~/.zshrc

  3. Verify Installation 

    git-drs --help

  4. Get Credentials

  5. Log in to your data commons (e.g., https://calypr-public.ohsu.edu/)
  6. Click your email → Profile → Create API Key → Download JSON
  7. Note the download path for later configuration

HPC Installation (Gen3 Server)

Target Environment: High-performance computing systems targeting Gen3 servers

Steps

  1. Install Git LFS on HPC 

    # Download and install Git LFS
wget https://github.com/git-lfs/git-lfs/releases/download/v3.7.1/git-lfs-linux-amd64-v3.7.1.tar.gz
tar -xvf git-lfs-linux-amd64-v3.7.1.tar.gz
export PREFIX=$HOME
./git-lfs-3.7.1/install.sh

# Make permanent
echo 'export PATH="$HOME/bin:$PATH"' >> ~/.bash_profile
source ~/.bash_profile

# Configure
git lfs install --skip-smudge

# Cleanup
rm git-lfs-linux-amd64-v3.7.0.tar.gz
rm -r git-lfs-3.7.0/

  2. Configure Git/SSH (if needed) 

    # Generate SSH key
ssh-keygen -t ed25519 -C "your_email@example.com"

# Add to ssh-agent
eval "$(ssh-agent -s)"
ssh-add ~/.ssh/id_ed25519

# Add public key to GitHub/GitLab
cat ~/.ssh/id_ed25519.pub

  3. Install Git DRS 

    /bin/bash -c "$(curl -fsSL https://raw.githubusercontent.com/calypr/git-drs/refs/heads/fix/install-error-macos/install.sh)"

# Update PATH
echo 'export PATH="$PATH:$HOME/.local/bin"' >> ~/.bash_profile
source ~/.bash_profile

  4. Verify Installation 

    git-drs version

Terra/Jupyter Installation (AnVIL Server)

Target Environment: Terra Jupyter notebooks targeting AnVIL DRS servers

Steps

  1. Launch Jupyter Environment in Terra

  2. Open Terminal in Jupyter

  3. Install Dependencies 

    # Install Git DRS
/bin/bash -c "$(curl -fsSL https://raw.githubusercontent.com/calypr/git-drs/refs/heads/fix/install-error-macos/install.sh)"

# Install DRS Downloader
wget https://github.com/anvilproject/drs_downloader/releases/download/0.1.6-rc.4/drs_downloader
chmod 755 drs_downloader

  4. Verify Installation 

    git-drs --help
drs_downloader --help

  5. Example Workflow 

    # Clone example repository
git clone https://github.com/quinnwai/super-cool-anvil-analysis.git
cd super-cool-anvil-analysis/

# Initialize and configure for your Terra project
git drs init
git drs remote add anvil development --terraProject $GOOGLE_PROJECT

# Work with manifests
gsutil cp $WORKSPACE_BUCKET/anvil-manifest.tsv .
git drs create-cache anvil-manifest.tsv

# List and pull files
git lfs ls-files
git lfs pull -I data_tables_sequencing_dataset.tsv

Local Installation (AnVIL Server)

Target Environment: Local development machine targeting AnVIL servers

Steps

  1. Install Git DRS (same as Gen3 local installation) 

    /bin/bash -c "$(curl -fsSL https://raw.githubusercontent.com/calypr/git-drs/refs/heads/fix/install-error-macos/install.sh)"

  2. Get Terra Project ID

  3. Log in to AnVIL Workspaces
  4. Select your workspace

  5. Copy the Google Project ID from "CLOUD INFORMATION"

  6. Configure AnVIL Access 

    # Check existing configuration
git drs remote list

# If no AnVIL server configured, add it
git drs init
git drs remote add anvil development --terraProject <your-terra-project-id>

Build from Source

For development or custom builds:

# Clone repository
git clone https://github.com/calypr/git-drs.git
cd git-drs

# Build
go build

# Make accessible
export PATH=$PATH:$(pwd)

Post-Installation

After installation, verify your setup:

# Check Git DRS version
git-drs version

# Check Git LFS
git lfs version

# View configured remotes (after setup)
git drs remote list

Next Steps

After installation, see:

Navigation: Installation → Getting Started → Commands Reference