Skip to content

README.md

Latest commit

 

History

History
154 lines (107 loc) · 4.65 KB

README.md

File metadata and controls

154 lines (107 loc) · 4.65 KB

DeepMASC Module System

This directory contains a module system for DeepMASC that allows you to run the tools without activating the conda environment or modifying your system PATH permanently.

Quick Start

The easiest way to set this up is to run the setup script:

cd <DeepMASC>/module
./setup.sh

Replace <DeepMASC> with your actual DeepMASC installation path.

The setup script will:

  1. Auto-detect your conda installation
  2. Auto-detect your module system directory
  3. Configure the wrapper scripts and module files
  4. Guide you through personal or system-wide installation

What's Included

Files

  • deepmasc.tcl - Tcl modulefile for Environment Modules
  • setup.sh - Interactive setup script (recommended)
  • uninstall.sh - Automatic uninstall script
  • INSTALL.md - Detailed installation instructions
  • bin/deepmasc - Wrapper script for main.py (AutoSelect3D)
  • bin/deepmasc-contour - Wrapper script for contour.py (AutoContour)
  • bin/deepmasc-relion-select - Wrapper for RELION AutoSelect3D
  • bin/deepmasc-relion-contour - Wrapper for RELION AutoContour
  • bin/deepmasc-relion-eval-mask - Wrapper for RELION Eval Refinement Mask

Commands

After installation, you'll have access to:

Standalone Commands:

  • deepmasc - Run AutoSelect3D to select the best 3D map
  • deepmasc-contour - Run AutoContour to generate masks

RELION Integration Commands:

  • deepmasc-relion-select - AutoSelect3D for RELION GUI (replaces gtf_relion4_run_select_class3d.py)
  • deepmasc-relion-contour - AutoContour for RELION GUI (replaces gtf_relion4_run_autocontour.py)
  • deepmasc-relion-eval-mask - Eval Refinement Mask for RELION GUI (replaces gtf_relion4_run_eval_refinement_mask.py)

Installation

Automatic Setup (Recommended)

./setup.sh

The setup script will auto-detect your system configuration and guide you through the installation process.

Manual Installation

See INSTALL.md for detailed manual installation instructions if you prefer to configure everything yourself.

Usage Examples

Standalone Usage

# Load the module
module load deepmasc

# AutoSelect3D - Select best map from multiple classes
deepmasc -f examples/Class3D/job016/run_it025_class*.mrc -g 0 -o output

# AutoContour - Generate masks
deepmasc-contour -i examples/Class3D/job016/run_it025_class001.mrc -o mask_output -g 0

# Unload when done
module unload deepmasc

RELION GUI Integration

After loading the module, you can use the wrapper commands in RELION's External job:

AutoSelect3D in RELION

External Executable: deepmasc-relion-select

Then in RELION GUI:

  • Input tab: Set "Input particles" to your Class3D/jobXXX/run_it025_data.star
  • Params tab: Add gpus parameter (e.g., 0 or 0,1)
  • Running tab: Set "Number of threads" to 1

AutoContour in RELION

External Executable: deepmasc-relion-contour

Then in RELION GUI:

  • Input tab: Set "Reference map" to your map file
  • Params tab: Add gpus parameter (e.g., 0)
  • Running tab: Set "Number of threads" to 1

Eval Refinement Mask in RELION

External Executable: deepmasc-relion-eval-mask

See the main README.md for detailed RELION integration instructions.

Requirements

  • DeepMASC conda environment must be created (conda env create -f environment.yml)
  • Environment Modules software must be installed (see INSTALL.md for installation instructions)

Troubleshooting

If you encounter issues, see the INSTALL.md file for troubleshooting tips, or:

  1. Verify conda environment exists: conda env list | grep DeepMASC
  2. Check Python path is correct in the wrapper scripts
  3. Ensure wrapper scripts are executable: ls -l bin/
  4. For modules: Check MODULEPATH includes this directory: echo $MODULEPATH

Customization

You can add more wrapper scripts for other Python scripts in the DeepMASC project:

  1. Create a new script in bin/ directory
  2. Copy the structure from existing wrapper scripts
  3. Update the Python script path
  4. Make it executable: chmod +x bin/your-new-command

Uninstallation

Automatic Uninstall (Recommended)

Run the automatic uninstall script:

cd <DeepMASC>/module
./uninstall.sh

The script will:

  • Auto-detect your installation type (personal or system-wide)
  • Remove module files and shell configuration entries
  • Provide clear instructions for any manual steps needed

Manual Uninstall

For detailed manual removal instructions, see INSTALL.md.

Support

For more information about DeepMASC itself, see the main README.md in the project root.