diff --git a/.github/workflows/test-downloads.yml b/.github/workflows/test-downloads.yml
new file mode 100644
index 0000000..1d3622e
--- /dev/null
+++ b/.github/workflows/test-downloads.yml
@@ -0,0 +1,57 @@
+name: Test Binary Downloads
+
+on:
+  push:
+    branches: [ main ]
+  pull_request:
+    branches: [ main ]
+  workflow_dispatch:
+
+permissions:
+  contents: read
+
+jobs:
+  test-downloads:
+    runs-on: ubuntu-latest
+    
+    steps:
+    - name: Checkout repository
+      uses: actions/checkout@v4
+      
+    - name: Set up Python
+      uses: actions/setup-python@v5
+      with:
+        python-version: '3.11'
+        
+    - name: Install Snakemake
+      run: |
+        pip install snakemake
+        
+    - name: Verify Snakefile syntax
+      run: |
+        snakemake --list-rules
+        
+    - name: Dry run workflow
+      run: |
+        snakemake --cores 1 --dry-run
+        
+    - name: Download and unpack binaries
+      run: |
+        make download
+        
+    - name: Verify downloaded binaries
+      run: |
+        ./verify_binaries.sh
+        
+    - name: Check binary versions
+      run: |
+        ./bin/plink1 --version || true
+        ./bin/plink2 --version || true
+        ./bin/regenie --version || true
+        
+    - name: Upload binaries as artifacts
+      uses: actions/upload-artifact@v4
+      with:
+        name: bioinformatics-binaries
+        path: bin/
+        retention-days: 7
diff --git a/.gitignore b/.gitignore
index b7faf40..628d30f 100644
--- a/.gitignore
+++ b/.gitignore
@@ -3,6 +3,13 @@ __pycache__/
 *.py[codz]
 *$py.class
 
+# Downloaded binaries and archives
+bin/
+downloads/
+
+# Snakemake
+.snakemake/
+
 # C extensions
 *.so
 
diff --git a/ADDING_BINARIES.md b/ADDING_BINARIES.md
new file mode 100644
index 0000000..dfa66e5
--- /dev/null
+++ b/ADDING_BINARIES.md
@@ -0,0 +1,64 @@
+# Adding New Binaries
+
+This document explains how to add new bioinformatics binaries to the workflow.
+
+## Steps to Add a New Binary
+
+1. **Find the download URL**: Locate the direct download URL for the Linux x86_64 version of the binary (usually a .zip file)
+
+2. **Edit config.yaml**: Add a new entry under `binaries:` following the existing pattern
+
+3. **Run the workflow**: Execute `make` or `snakemake --cores 1` to download the new binary
+
+## Example: Adding bcftools
+
+To add bcftools to the workflow, edit `config.yaml`:
+
+```yaml
+binaries:
+  # ... existing entries ...
+  
+  bcftools:
+    version: "1.19"
+    url: "https://github.com/samtools/bcftools/releases/download/1.19/bcftools-1.19-linux-x86_64.tar.bz2"
+    executable: "bcftools"
+    description: "BCFtools - utilities for variant calling and manipulating VCFs and BCFs"
+```
+
+Then run:
+```bash
+make bcftools
+```
+
+Or to download all binaries including the new one:
+```bash
+make
+```
+
+## Configuration Fields
+
+- `version`: Version number of the binary (for documentation purposes)
+- `url`: Direct download URL for the binary archive
+- `executable`: Name of the executable file inside the archive (before renaming)
+- `description`: Brief description of the tool (optional, for documentation)
+
+## Supported Archive Formats
+
+Currently, the workflow supports:
+- `.zip` files (using unzip)
+
+To add support for other formats (e.g., `.tar.gz`, `.tar.bz2`), modify the `unpack_binary` rule in the Snakefile.
+
+## Testing
+
+After adding a new binary, test it:
+
+1. **Dry run**: `snakemake bin/BINARY_NAME --cores 1 --dry-run`
+2. **Download**: `snakemake bin/BINARY_NAME --cores 1`
+3. **Verify**: `./verify_binaries.sh` (after updating the script to check the new binary)
+
+## Troubleshooting
+
+- **Wrong executable name**: If the unpacked executable has a different name than expected, adjust the `executable` field in `config.yaml`
+- **Archive format not supported**: Modify the `unpack_binary` rule in `Snakefile` to handle the new format
+- **Download fails**: Verify the URL is correct and accessible
diff --git a/Makefile b/Makefile
new file mode 100644
index 0000000..379a704
--- /dev/null
+++ b/Makefile
@@ -0,0 +1,48 @@
+# Makefile for managing bioinformatics binaries
+
+.PHONY: all download clean help test
+
+# Default target
+all: download
+
+# Download and unpack all binaries
+download:
+	@echo "Downloading and unpacking binaries..."
+	snakemake --cores 1
+
+# Download specific binaries
+plink1:
+	snakemake bin/plink1 --cores 1
+
+plink2:
+	snakemake bin/plink2 --cores 1
+
+regenie:
+	snakemake bin/regenie --cores 1
+
+# Clean downloaded files and binaries
+clean:
+	@echo "Cleaning downloaded files..."
+	rm -rf bin/ downloads/
+	rm -rf .snakemake/
+
+# Show what would be downloaded
+dry-run:
+	snakemake --cores 1 --dry-run
+
+# List all rules
+list:
+	snakemake --list-rules
+
+# Show help
+help:
+	@echo "Available targets:"
+	@echo "  all       - Download and unpack all binaries (default)"
+	@echo "  download  - Download and unpack all binaries"
+	@echo "  plink1    - Download and unpack PLINK1 only"
+	@echo "  plink2    - Download and unpack PLINK2 only"
+	@echo "  regenie   - Download and unpack regenie only"
+	@echo "  clean     - Remove downloaded files and binaries"
+	@echo "  dry-run   - Show what would be downloaded without actually downloading"
+	@echo "  list      - List all available rules"
+	@echo "  help      - Show this help message"
diff --git a/README.md b/README.md
index 9c1f894..f47debb 100644
--- a/README.md
+++ b/README.md
@@ -1,2 +1,161 @@
 # tsd_software
 Scripts to fetch specific binaries to be synced to TSD's s3-api dir
+
+## Overview
+
+This repository contains Snakemake workflows to download and unpack bioinformatics binaries including:
+- **PLINK1** - Whole genome association analysis toolset (version 20250819)
+- **PLINK2** - Next generation of PLINK (version 20251019)
+- **regenie** - Fast whole genome regression modelling (version 4.1)
+
+## Requirements
+
+- Python 3.6+
+- Snakemake
+- curl (for downloading)
+- unzip (for unpacking archives)
+
+## Installation
+
+Install Snakemake using pip in the current Python environment:
+```bash
+pip install snakemake
+```
+
+Or using conda/mamba:
+```bash
+mamba install -c conda-forge -c bioconda snakemake
+```
+
+Or using the provided conda environment file:
+```bash
+conda env create -f environment.yaml
+conda activate tsd_software
+```
+
+## Usage
+
+### Using Make (recommended)
+
+The easiest way to use this workflow is via the provided Makefile:
+
+```bash
+# Download and unpack all binaries
+make
+
+# Download specific binaries
+make plink1
+make plink2
+make regenie
+
+# Show what would be downloaded without downloading
+make dry-run
+
+# Clean all downloaded files
+make clean
+
+# Show available commands
+make help
+```
+
+### Using Snakemake directly
+
+Run the workflow to download and unpack all binaries:
+```bash
+snakemake --cores 1
+```
+
+Download specific binaries:
+```bash
+snakemake bin/plink1 --cores 1
+snakemake bin/plink2 --cores 1
+snakemake bin/regenie --cores 1
+```
+
+Perform a dry run to see what would be downloaded:
+```bash
+snakemake --cores 1 --dry-run
+```
+
+Clean downloaded files:
+```bash
+rm -rf bin/ downloads/
+```
+
+### Verifying Downloads
+
+After downloading, verify the binaries are correctly installed:
+```bash
+./verify_binaries.sh
+```
+
+This will check that all binaries exist, are executable, and display version information.
+
+## Configuration
+
+Binary versions and download URLs are configured in `config.yaml`. To update a binary version:
+
+1. Edit `config.yaml`
+2. Update the `version` and `url` fields for the desired binary
+3. Run `make clean` to remove old binaries
+4. Run `make` to download the new version
+
+Example configuration entry:
+```yaml
+binaries:
+  plink1:
+    version: "20231211"
+    url: "https://s3.amazonaws.com/plink1-assets/plink_linux_x86_64_20231211.zip"
+    executable: "plink"
+    description: "PLINK 1.9 - Whole genome association analysis toolset"
+```
+
+## Output
+
+Binaries are downloaded to the `bin/` directory in the repository root:
+- `bin/plink1` - PLINK 1.9 executable
+- `bin/plink2` - PLINK 2.0 executable  
+- `bin/regenie` - regenie executable
+
+Downloaded archives are stored in the `downloads/` directory (can be safely deleted after unpacking).
+
+## Workflow Structure
+
+The Snakemake workflow consists of:
+
+1. **download_binary** - Downloads binary archives from configured URLs
+2. **unpack_binary** - Unpacks archives and renames executables as needed
+3. **all** - Default rule that downloads and unpacks all binaries
+
+The workflow automatically:
+- Creates necessary directories (`bin/`, `downloads/`)
+- Downloads archives only if not already present
+- Unpacks binaries only if not already present
+- Makes binaries executable
+- Handles renaming of executables to standard names
+
+## Troubleshooting
+
+### Download failures
+If downloads fail, check:
+- Internet connectivity
+- The URLs in `config.yaml` are still valid
+- You have write permissions in the repository directory
+
+### Binary not executable
+If a binary exists but is not executable, run:
+```bash
+chmod +x bin/plink1 bin/plink2 bin/regenie
+```
+
+### Re-downloading binaries
+To force re-download of binaries:
+```bash
+make clean
+make
+```
+
+## License
+
+See LICENSE file for details.
+
diff --git a/Snakefile b/Snakefile
new file mode 100644
index 0000000..f6975bd
--- /dev/null
+++ b/Snakefile
@@ -0,0 +1,44 @@
+"""
+Snakemake workflow to download and unpack bioinformatics binaries.
+Downloads PLINK1, PLINK2, and regenie to the bin/ directory.
+"""
+
+configfile: "config.yaml"
+
+# Get list of binaries from config
+BINARIES = list(config["binaries"].keys())
+
+# Default rule - download and unpack all binaries
+rule all:
+    input:
+        expand("bin/{binary}", binary=BINARIES)
+
+# Rule to download a binary archive
+rule download_binary:
+    output:
+        "downloads/{binary}.zip"
+    params:
+        url = lambda wildcards: config["binaries"][wildcards.binary]["url"]
+    shell:
+        """
+        mkdir -p downloads
+        curl -L -o {output} {params.url}
+        """
+
+# Rule to unpack a binary archive
+rule unpack_binary:
+    input:
+        "downloads/{binary}.zip"
+    output:
+        "bin/{binary}"
+    params:
+        executable = lambda wildcards: config["binaries"][wildcards.binary]["executable"]
+    shell:
+        """
+        mkdir -p bin
+        unzip -o {input} -d bin/
+        if [ "{params.executable}" != "{wildcards.binary}" ]; then
+            mv bin/{params.executable} {output}
+        fi
+        chmod +x {output}
+        """
diff --git a/WORKFLOW_DIAGRAM.md b/WORKFLOW_DIAGRAM.md
new file mode 100644
index 0000000..97dcbd1
--- /dev/null
+++ b/WORKFLOW_DIAGRAM.md
@@ -0,0 +1,173 @@
+# Workflow Diagram
+
+## Repository Structure
+
+```
+tsd_software/
+├── .github/
+│   └── workflows/
+│       └── test-downloads.yml    # CI/CD workflow for automated testing
+├── bin/                          # Output: Downloaded binaries (gitignored)
+│   ├── plink1                    # PLINK 1.9 executable
+│   ├── plink2                    # PLINK 2.0 executable
+│   └── regenie                   # regenie executable
+├── downloads/                    # Temporary: Downloaded archives (gitignored)
+│   ├── plink1.zip
+│   ├── plink2.zip
+│   └── regenie.zip
+├── Snakefile                     # Main workflow definition
+├── config.yaml                   # Binary configuration (URLs, versions)
+|-- environment.yaml              # conda environment file
+├── Makefile                      # Convenience interface
+├── verify_binaries.sh            # Binary verification script
+├── example_usage.sh              # Usage demonstration
+├── test_workflow.sh              # Comprehensive test suite
+├── README.md                     # Main documentation
+├── ADDING_BINARIES.md            # Guide for adding new binaries
+├── .gitignore                    # Excludes bin/, downloads/, .snakemake/
+└── LICENSE                       # License file
+```
+
+## Workflow Flow
+
+```
+User Command
+    ↓
+make / snakemake
+    ↓
+    ├─→ Read config.yaml (binary definitions)
+    │
+    ├─→ download_binary (for each binary)
+    │   └─→ curl → downloads/{binary}.zip
+    │
+    ├─→ unpack_binary (for each binary)
+    │   └─→ unzip → bin/{binary}
+    │           └─→ chmod +x
+    │
+    └─→ all (final rule)
+        └─→ bin/plink1, bin/plink2, bin/regenie ✓
+```
+
+## Data Flow
+
+```
+config.yaml
+    ↓ (defines)
+Binary URLs & Versions
+    ↓ (downloads)
+downloads/*.zip
+    ↓ (unpacks)
+bin/plink1, bin/plink2, bin/regenie
+    ↓ (verified by)
+verify_binaries.sh
+```
+
+## Snakemake Rules
+
+```
+┌────────────────────────────────────────┐
+│         rule: all (default)            │
+│  input: bin/plink1, bin/plink2,       │
+│         bin/regenie                    │
+└───────────────┬────────────────────────┘
+                │
+        ┌───────┴───────┬────────────┐
+        │               │            │
+        ▼               ▼            ▼
+┌──────────────┐ ┌──────────────┐ ┌──────────────┐
+│ unpack_binary│ │ unpack_binary│ │ unpack_binary│
+│  plink1      │ │  plink2      │ │  regenie     │
+└──────┬───────┘ └──────┬───────┘ └──────┬───────┘
+       │                │                │
+       ▼                ▼                ▼
+┌──────────────┐ ┌──────────────┐ ┌──────────────┐
+│download_     │ │download_     │ │download_     │
+│binary plink1 │ │binary plink2 │ │binary regenie│
+└──────────────┘ └──────────────┘ └──────────────┘
+```
+
+## User Interaction Paths
+
+### Path 1: Download All Binaries
+```bash
+make                          # User command
+  → snakemake --cores 1       # Executes workflow
+    → Downloads all binaries
+    → Unpacks to bin/
+```
+
+### Path 2: Download Specific Binary
+```bash
+make plink1                              # User command
+  → snakemake bin/plink1 --cores 1      # Executes workflow
+    → Downloads plink1.zip
+    → Unpacks to bin/plink1
+```
+
+### Path 3: Dry Run (Validation)
+```bash
+make dry-run                   # User command
+  → snakemake --dry-run        # Shows what would be done
+    → No actual downloads
+    → Reports planned actions
+```
+
+### Path 4: Verification
+```bash
+./verify_binaries.sh           # User command
+  → Checks bin/ directory
+  → Verifies executability
+  → Shows version info
+```
+
+## Configuration Extension
+
+To add a new binary (e.g., samtools):
+
+1. Edit `config.yaml`:
+```yaml
+binaries:
+  # ... existing entries ...
+  samtools:
+    version: "1.19"
+    url: "https://github.com/samtools/samtools/releases/download/1.19/samtools-1.19-linux-x86_64.tar.bz2"
+    executable: "samtools"
+    description: "SAM/BAM file manipulation"
+```
+
+2. Run:
+```bash
+make samtools
+```
+
+3. Binary appears at `bin/samtools`
+
+## CI/CD Pipeline
+
+```
+GitHub Event (push/PR)
+    ↓
+.github/workflows/test-downloads.yml
+    ↓
+    ├─→ Setup Python & Snakemake
+    ├─→ Verify Snakefile syntax
+    ├─→ Run dry-run
+    ├─→ Download all binaries
+    ├─→ Verify binaries
+    └─→ Upload as artifacts ✓
+```
+
+## Testing Hierarchy
+
+```
+test_workflow.sh
+    ├─→ Test 1: File existence
+    ├─→ Test 2: Snakefile syntax
+    ├─→ Test 3: config.yaml validity
+    ├─→ Test 4: Binary configuration
+    ├─→ Test 5: Workflow dry-run
+    ├─→ Test 6: Makefile targets
+    └─→ Test 7: Script permissions
+```
+
+All tests must pass for the workflow to be considered functional.
diff --git a/config.yaml b/config.yaml
new file mode 100644
index 0000000..6b88abd
--- /dev/null
+++ b/config.yaml
@@ -0,0 +1,21 @@
+# Configuration file for bioinformatics binaries
+# Defines download URLs and versions for each tool
+
+binaries:
+  plink1:
+    version: "20250819"
+    url: "https://s3.amazonaws.com/plink1-assets/plink_linux_x86_64_20250819.zip"
+    executable: "plink"
+    description: "PLINK 1.9 - Whole genome association analysis toolset"
+  
+  plink2:
+    version: "20251019"
+    url: "https://s3.amazonaws.com/plink2-assets/plink2_linux_amd_avx2_20251019.zip"
+    executable: "plink2"
+    description: "PLINK 2.0 - Next generation of PLINK"
+  
+  regenie:
+    version: "v4.1"
+    url: "https://github.com/rgcgithub/regenie/releases/download/v4.1/regenie_v4.1.gz_x86_64_Linux_mkl.zip"
+    executable: "regenie_v4.1.gz_x86_64_Linux_mkl"
+    description: "regenie - Fast whole genome regression modelling"
diff --git a/environment.yaml b/environment.yaml
new file mode 100644
index 0000000..b2a8057
--- /dev/null
+++ b/environment.yaml
@@ -0,0 +1,13 @@
+name: tsd_software
+channels:
+  - conda-forge
+  - bioconda
+  - defaults
+dependencies:
+  - python>=3.8
+  - snakemake>=7.0
+  - curl
+  - unzip
+  - pip
+  - pip:
+    - pyyaml
diff --git a/example_usage.sh b/example_usage.sh
new file mode 100755
index 0000000..8a8a6cb
--- /dev/null
+++ b/example_usage.sh
@@ -0,0 +1,72 @@
+#!/bin/bash
+# Example usage script for the bioinformatics binary download workflow
+# This script demonstrates various ways to use the workflow
+
+set -e
+
+echo "=============================================="
+echo "Bioinformatics Binary Download Workflow Demo"
+echo "=============================================="
+echo ""
+
+# Show help
+echo "1. Showing available make targets:"
+echo "   $ make help"
+echo ""
+make help
+echo ""
+
+# Dry run
+echo "2. Performing a dry-run to see what would be downloaded:"
+echo "   $ make dry-run"
+echo ""
+make dry-run
+echo ""
+
+# List rules
+echo "3. Listing all Snakemake rules:"
+echo "   $ make list"
+echo ""
+make list
+echo ""
+
+# Show configuration
+echo "4. Current binary configuration:"
+echo "   $ cat config.yaml"
+echo ""
+cat config.yaml
+echo ""
+
+# Download instructions (not executed due to network limitations)
+echo "5. To download all binaries (when internet is available):"
+echo "   $ make"
+echo "   or"
+echo "   $ make download"
+echo ""
+
+echo "6. To download a specific binary:"
+echo "   $ make plink1"
+echo "   $ make plink2"
+echo "   $ make regenie"
+echo ""
+
+echo "7. To verify downloaded binaries (after download):"
+echo "   $ ./verify_binaries.sh"
+echo ""
+
+echo "8. To clean all downloaded files:"
+echo "   $ make clean"
+echo ""
+
+echo "9. Using Snakemake directly:"
+echo "   $ snakemake --cores 1                 # Download all"
+echo "   $ snakemake bin/plink1 --cores 1      # Download PLINK1 only"
+echo "   $ snakemake --cores 1 --dry-run       # Dry run"
+echo ""
+
+echo "=============================================="
+echo "For more information, see:"
+echo "  - README.md for general usage"
+echo "  - ADDING_BINARIES.md for adding new tools"
+echo "  - config.yaml for binary configuration"
+echo "=============================================="
diff --git a/test_workflow.sh b/test_workflow.sh
new file mode 100755
index 0000000..3bfceb2
--- /dev/null
+++ b/test_workflow.sh
@@ -0,0 +1,139 @@
+#!/bin/bash
+# Comprehensive test of the workflow implementation
+
+echo "====================================="
+echo "Testing Snakemake Workflow"
+echo "====================================="
+echo ""
+
+# Test 1: Check files exist
+echo "Test 1: Verifying all required files exist..."
+files=(
+    "Snakefile"
+    "config.yaml"
+    "Makefile"
+    "README.md"
+    "ADDING_BINARIES.md"
+    "verify_binaries.sh"
+    "example_usage.sh"
+    ".github/workflows/test-downloads.yml"
+)
+
+all_exist=true
+for file in "${files[@]}"; do
+    if [ -f "$file" ]; then
+        echo "  ✓ $file"
+    else
+        echo "  ✗ $file (MISSING)"
+        all_exist=false
+    fi
+done
+
+if [ "$all_exist" = true ]; then
+    echo "  Result: PASSED"
+else
+    echo "  Result: FAILED"
+    exit 1
+fi
+echo ""
+
+# Test 2: Check Snakefile syntax
+echo "Test 2: Checking Snakefile syntax..."
+if snakemake --list-rules > /dev/null 2>&1; then
+    echo "  ✓ Snakefile syntax valid"
+    echo "  Result: PASSED"
+else
+    echo "  ✗ Snakefile has syntax errors"
+    echo "  Result: FAILED"
+    exit 1
+fi
+echo ""
+
+# Test 3: Check config.yaml is valid
+echo "Test 3: Checking config.yaml validity..."
+python3 -c "import yaml; yaml.safe_load(open('config.yaml'))" 2>/dev/null
+if [ $? -eq 0 ]; then
+    echo "  ✓ config.yaml is valid YAML"
+    echo "  Result: PASSED"
+else
+    echo "  ✗ config.yaml has syntax errors"
+    echo "  Result: FAILED"
+    exit 1
+fi
+echo ""
+
+# Test 4: Verify binaries in config
+echo "Test 4: Checking configured binaries..."
+binaries=$(python3 -c "import yaml; c=yaml.safe_load(open('config.yaml')); print(','.join(c['binaries'].keys()))")
+echo "  Configured binaries: $binaries"
+expected="plink1,plink2,regenie"
+if [ "$binaries" = "$expected" ]; then
+    echo "  ✓ All expected binaries configured"
+    echo "  Result: PASSED"
+else
+    echo "  ✗ Unexpected binaries (expected: $expected)"
+    echo "  Result: FAILED"
+    exit 1
+fi
+echo ""
+
+# Test 5: Dry run
+echo "Test 5: Running workflow dry-run..."
+if snakemake --cores 1 --dry-run > /dev/null 2>&1; then
+    echo "  ✓ Dry run successful"
+    echo "  Result: PASSED"
+else
+    echo "  ✗ Dry run failed"
+    echo "  Result: FAILED"
+    exit 1
+fi
+echo ""
+
+# Test 6: Check Makefile targets
+echo "Test 6: Checking Makefile targets..."
+targets=("help" "list" "dry-run")
+all_work=true
+for target in "${targets[@]}"; do
+    if make $target > /dev/null 2>&1; then
+        echo "  ✓ make $target"
+    else
+        echo "  ✗ make $target (FAILED)"
+        all_work=false
+    fi
+done
+
+if [ "$all_work" = true ]; then
+    echo "  Result: PASSED"
+else
+    echo "  Result: FAILED"
+    exit 1
+fi
+echo ""
+
+# Test 7: Check scripts are executable
+echo "Test 7: Checking script permissions..."
+scripts=("verify_binaries.sh" "example_usage.sh")
+all_exec=true
+for script in "${scripts[@]}"; do
+    if [ -x "$script" ]; then
+        echo "  ✓ $script is executable"
+    else
+        echo "  ✗ $script is not executable"
+        all_exec=false
+    fi
+done
+
+if [ "$all_exec" = true ]; then
+    echo "  Result: PASSED"
+else
+    echo "  Result: FAILED"
+    exit 1
+fi
+echo ""
+
+echo "====================================="
+echo "All tests PASSED!"
+echo "====================================="
+echo ""
+echo "The Snakemake workflow is ready to use."
+echo "Run 'make' or 'snakemake --cores 1' to download binaries."
diff --git a/verify_binaries.sh b/verify_binaries.sh
new file mode 100755
index 0000000..32847a3
--- /dev/null
+++ b/verify_binaries.sh
@@ -0,0 +1,68 @@
+#!/bin/bash
+# Script to verify downloaded binaries
+
+set -e
+
+BIN_DIR="bin"
+
+echo "Verifying downloaded binaries..."
+echo "================================"
+
+# Check if bin directory exists
+if [ ! -d "$BIN_DIR" ]; then
+    echo "ERROR: bin/ directory not found. Run 'make download' first."
+    exit 1
+fi
+
+# Function to check a binary
+check_binary() {
+    local name=$1
+    local path="$BIN_DIR/$name"
+    
+    echo -n "Checking $name... "
+    if [ -f "$path" ]; then
+        if [ -x "$path" ]; then
+            echo "✓ Found and executable"
+            # Try to get version info
+            case $name in
+                plink1)
+                    "$path" --version 2>&1 | head -1 || echo "  (version info unavailable)"
+                    ;;
+                plink2)
+                    "$path" --version 2>&1 | head -1 || echo "  (version info unavailable)"
+                    ;;
+                regenie)
+                    "$path" --version 2>&1 | head -1 || echo "  (version info unavailable)"
+                    ;;
+            esac
+        else
+            echo "✗ Found but not executable"
+            return 1
+        fi
+    else
+        echo "✗ Not found"
+        return 1
+    fi
+}
+
+# Check all binaries
+PASSED=0
+FAILED=0
+
+# Disable exit on error
+set +e
+
+for binary in plink1 plink2 regenie; do
+    if check_binary "$binary"; then
+        ((PASSED++))
+    else
+        ((FAILED++))
+    fi
+done
+
+echo ""
+echo "Results: $PASSED passed, $FAILED failed"
+
+if [ $FAILED -gt 0 ]; then
+    exit 1
+fi