Using the Graphical User Interface (GUI) - ChromatinCloud/SeqForge GitHub Wiki

This article provides an overview of the BaseBuddy GUI, explaining how to launch it and how to use its features.

  1. Overview

For users who prefer a visual and interactive workflow, BaseBuddy provides a desktop Graphical User Interface (GUI). The GUI exposes the core functionality of the toolkit in an easy-to-use format, eliminating the need to memorize command-line syntax.

The GUI is ideal for:

Quickly setting up and running simulation tasks.
Interactively exploring the parameters available for each tool.
Users less comfortable with a terminal-based environment.
Educational demonstrations of sequencing simulation.
  1. Launching the GUI

Prerequisites:

A full BaseBuddy installation via the Conda method, which ensures all dependencies, including the GUI library customtkinter, are present.
An active basebuddy Conda environment.
A desktop environment (the GUI cannot be run on a headless server).

Launch Command: Open your terminal, activate the Conda environment (mamba activate basebuddy), and run: Bash

python -m src.basebuddy.gui.main_app

This will open the main BaseBuddy application window. 3. GUI Features

The GUI is organized into tabs, each corresponding to a major BaseBuddy function.

Short-Read Simulation: A graphical front-end for the basebuddy short command. Use file dialogs to select your FASTA and output directory, and use sliders and dropdowns to set depth, read length, and the ART profile.
Long-Read Simulation: An interface for the basebuddy long command. Select your FASTA, set the sequencing depth, and choose a NanoSim-h model.
Variant Spiking: A powerful interface for basebuddy spike. Provides file selection buttons for the reference, input BAM(s), and VCFs. Includes fields for VAF, the random seed, and the required path to picard.jar.
Apply Signature to FASTA: Exposes the internal function for creating a mutated FASTA file. Select an input FASTA, choose a signature (e.g., 'SBS1') from a bundled list, set the number of mutations, and specify an output file path.
Read Quality Control (FastQC): An interface for basebuddy qc. Allows you to select multiple FASTQ files, set the number of threads, and choose an output directory for the reports.

Common Elements:

Run Button: Each tab has a "Run" button to execute the specified task.
Status Log & Progress Bar: A log at the bottom of the window shows the status of running commands, and a progress bar provides visual feedback during execution.
Help Tooltips: Hovering over an option reveals a tooltip explaining its purpose.