lmodify 0.3.0

LMODify: Create LMOD packages based on Singularity images for HPC environments

lmodify

A Python CLI tool for creating and managing LMOD modules from Singularity/Apptainer containers in HPC environments.

Features

• Automatic package name and version detection from Singularity image filenames
• Generate LMOD Lua module files
• Create wrapper scripts for containerized applications
• Manage multiple package versions
• Add commands to existing packages
• Interactive configuration setup

Installation

pip install -e .

For development:

pip install -e ".[dev]"

Quick Start

1. Initialize Configuration

First, create your configuration file:

lmodify init

This will prompt you for:

• Path to Singularity images
• Path for binary wrappers
• Path for LMOD Lua files
• Your metadata (name, email, organization)

The configuration is saved to ~/.config/lmodify.ini by default.

2. Create a Package

Create an LMOD module from a Singularity image:

lmodify create -s /path/to/seqfu__1.20.3.simg seqfu fu-msa fu-orf

Or load commands from a file:

lmodify create -s /path/to/seqfu__1.20.3.simg -f commands.txt

This will:

1. Parse the package name and version from the image filename
2. Create a wrapper script in {bin_path}/seqfu__1.20.3/singularity.exec
3. Create symlinks for the specified commands
4. Generate an LMOD Lua file at {lmod_path}/seqfu/1.20.3.lua

3. List Available Packages

View all available LMOD modules:

lmodify list

Filter by keyword:

lmodify list seqfu

Show only package names:

lmodify list -p

4. Add Commands to Existing Packages

Add one or more commands to an existing package:

lmodify add seqfu fu-orf
lmodify add seqfu fu-orf fu-shred fu-pecheck

Add from a file:

lmodify add seqfu -f commands.txt

Add to a specific version:

lmodify add seqfu fu-orf --version 1.20.3

Supported Image Naming Patterns

lmodify automatically detects package names and versions from these patterns:

1. Galaxy Project depot pattern:

   depot.galaxyproject.org-singularity-{name}-{version}--{build}.img
   depot.galaxyproject.org-singularity-kraken2-2.0.8_beta--pl526hc9558a2_2.img
   

2. Colon pattern:

   {name}:{version}--{build}
   checkv:1.0.3--pyhdfd78af_0
   genomad:1.9.0--pyhdfd78af_1.simg
   

3. Double underscore pattern:

   {name}__{version}[.extension]
   seqfu__1.20.3
   unicycler__0.5.1.simg
   

If automatic detection fails, you can specify manually:

lmodify create -s image.sif -p mypackage -v 1.0.0 mycommand

Commands

init

Create a configuration file with interactive prompts.

lmodify init [-o OUTPUT] [-f]

Options:

• -o, --output: Output path for config file
• -f, --force: Overwrite existing config file

create

Create a new LMOD package from a Singularity image.

lmodify create [OPTIONS] [COMMANDS...]

Options:

• -s, --singularity: Path to Singularity image (required)
• -p, --package: Package name (auto-detected if not provided)
• -v, --version: Package version (auto-detected if not provided)
• -f, --cmd-file: File with list of commands (one per line, # for comments)
• -l, --lmod-path: Override LMOD path from config
• -b, --bin-path: Override bin path from config
• -d, --description: Package description
• -C, --category: Package category (bio, chem, physics, tools, etc.)
• --force: Overwrite existing files
• --dry-run: Preview without making changes

Command file format:

Create a text file with one command per line. Empty lines and lines starting with # are ignored:

# Core commands
seqfu
fu-msa
fu-orf
fu-index
fu-shred

# Additional utilities
fu-pecheck
fu-tabcheck

You can combine commands from both the file and command-line arguments. Duplicates are automatically removed.

list

List available LMOD packages.

lmodify list [KEYWORD] [-p]

Options:

• KEYWORD: Filter packages (case-insensitive)
• -p, --packages-only: Show only package names, not versions
• -l, --lmod-path: Override LMOD path from config

add

Add one or more commands to an existing package.

lmodify add PACKAGE [COMMANDS...] [OPTIONS]

Options:

• -f, --cmd-file: File with list of commands (one per line, # for comments)
• -v, --version: Add to specific version (default: all versions)
• -l, --lmod-path: Override LMOD path from config
• -b, --bin-path: Override bin path from config
• --force: Overwrite existing command
• --dry-run: Preview without making changes

Examples:

# Add single command
lmodify add seqfu fu-orf

# Add multiple commands
lmodify add seqfu fu-orf fu-shred fu-pecheck

# Add from file
lmodify add seqfu -f commands.txt

# Combine file and arguments
lmodify add seqfu fu-extra -f commands.txt --version 1.20.3

Configuration File

Default location: ~/.config/lmodify.ini

[lmodify]
singularity_default_path = /opt/singularity
bin_path = /opt/bin
lmod_path = /opt/lmod

[metadata]
author = Your Name
email = [e-mail]
organization = Your Organization

You can specify a custom config file with:

lmodify -c /path/to/config.ini <command>

How It Works

When you create a package, lmodify:

1. Creates a wrapper script (singularity.exec) that executes commands inside the container:

   #!/bin/bash
   singularity exec "/path/to/image.simg" $(basename "$0") "$@"
   

2. Creates symlinks for each command pointing to the wrapper script:

   seqfu -> singularity.exec
   stats -> singularity.exec
   

3. Generates an LMOD Lua module that adds the bin directory to PATH:

   prepend_path("PATH", "/opt/bin/seqfu__1.20.3")
   

Users can then load the module:

module load seqfu/1.20.3
seqfu --version

Development

Run tests:

pytest

Run tests with coverage:

pytest --cov=lmodify

License

MIT License

Contributing

Contributions are welcome! Please feel free to submit a Pull Request.