rc

A command line tool to run various biomolecular structural prediction, analysis and design applications using containerized environments.

Overview

rc provides a unified interface for running Rosetta and other biomolecular modeling applications through container engines like Docker, Singularity, or Apptainer.

Installation

cargo install --path .

Basic Usage

Running Rosetta Score

Score a PDB structure file using Rosetta:

rc run -w /path/to/working/directory rosetta score \
    -out:file:scorefile output.sc \
    -in:file:s structure.pdb

This command will:

• Use the default Docker container engine
• Mount the working directory into the container
• Run the Rosetta score application
• Output the score file to output.sc
• Log the executed command to a log file for reproducibility

Specifying a Container Engine

You can specify which container engine to use with the -e flag:

rc run -e singularity rosetta score -in:file:s structure.pdb

Supported container engines:

• docker (default)
• singularity
• apptainer
• none (run natively without containers)

Working Directory

The -w flag specifies the working directory that will be mounted into the container:

rc run -w ./data rosetta score -in:file:s input.pdb

If not specified, the current directory (.) is used by default.

Command Logging

Every command executed by rc is automatically logged to an appropriate log file. This provides:

• Reproducibility - Review and replay exact commands that were run
• Debugging - Trace what commands were executed in case of issues
• Documentation - Keep a record of all operations performed

The log files are stored in the working directory and contain the full command line that was executed, including all arguments passed to the containerized application.

Commands

run

Run an application with optional arguments.

rc run [OPTIONS] <APP> [ARGS]...

Options:

• -w, --working-dir <PATH> - Input directory path (default: current directory)
• -e, --container-engine <ENGINE> - Container engine to use (default: docker)

Available Apps:

• rosetta - Run Rosetta protocol
• score - Run Rosetta score command

install

Install an application (not yet implemented).

rc install <APP>

clean

Clean an app installation (not yet implemented).

rc clean <APP>

Examples

Score a single structure

rc run rosetta score \
    -out:file:scorefile my_scores.sc \
    -in:file:s my_protein.pdb

Using with different working directory

rc run -w /data/structures rosetta score \
    -out:file:scorefile results/scores.sc \
    -in:file:s protein.pdb

Using Singularity instead of Docker

rc run -e singularity rosetta score \
    -in:file:s structure.pdb

Verbose Mode

Enable verbose output with the -v flag:

rc -v run rosetta score -in:file:s structure.pdb

This will show detailed information including the exact command being executed and where it's being logged.

Requirements

• One of the supported container engines (Docker, Singularity, or Apptainer)
• Appropriate container images for the applications you want to run

License

See LICENSE file for details.

Author

Sergey Lyskov