/r2g_gui

A GUI for r2g, which is a homology-based, computationally lightweight pipeline for discovering genes in the absence of an assembly

Primary LanguagePythonMIT LicenseMIT

Reads to Genes (r2g) GUI

PyPI py_ver licence

Introduction

screenshot

This is the GUI wrapper for Reads to Genes, or r2g, which is a homology-based, computationally lightweight pipeline for discovering genes in the absence of an assembly. The r2g core is hosted on https://github.com/yangwu91/r2g.

The r2g GUI is still under developing, please feel free to file an issue or email me.

Implementation

Install Docker

Please follow the instruction here to download and install Docker based on your operating system before running the r2g GUI. The Docker software is compatible with most common operating systems including Linux, macOS and Windows.

Install r2g GUI

You can choose one of the following methods to install the r2g GUI:

  • Download zipped pre-built binary files (Python 3 environment is NOT required)

    Operating System Size (MB) MD5 Download link
    Windows 38.1 78f3428a1f3305015f17255ef9536b46 r2g_gui-0.1.1-Windows.zip
    macOS (Intel Chip) 28.7 f04b80a1f8a08e57ea8230f2e9af2c12 r2g_gui-0.1.1-macOS.zip

    ⚠️ Please note that Windows Defender will report it as Trojan:Win32/Wacatac.B!ml, which is false positive. Add the r2g.exe to the excluding list of Windows Defender for further use. Please check out the scanning results on https://virustotal.com. Or maybe you can try the other method if the Python 3 environment has been installed on your computer.

    windows_defender

    ⚠️ Please note that the executable binary has not been tested on the Apple M1 Chip.

  • Install by PyPI (Python 3 environment is required)

    If Python 3 and the pip utility has been installed on your computer, the r2g GUI can be installed by the command as follows:

    pip install r2g_gui

Usage

  1. Please run the Docker (i.e. Docker Desktop on Windows/macOS or Docker Deamon on Linux) before start the r2g job.

  2. Start the r2g GUI. At the first time, the r2g GUI will pull the latest image of the r2g Docker, which should take a while depending on your network quality.

    • Windows

      Unzip the r2g_gui-*.*.*-Windows.zip, and then double click r2g.exe.

      win

    • macOS

      Unzip the r2g_gui-*.*.*-macOS.zip. Hold Control and click r2g.app, or right click r2g.app, then click open.

      mac

    • Other systems with Python 3 environment (installed by PyPI)

      Simply typing r2g.gui.py in the terminal should call the r2g GUI.

  3. Fill in the parameters and hit the Start! button to submit the job. In addition, here is an example configuration. To use it, please click File -> Import parameters... and then select it, the GUI wrapper will load pre-configured parameters automatically. Hit the Start! button and enjoy!

Tweak parameters

The r2g GUI is the GUI wrapper for the r2g, please check out the detailed usage of r2g to tweak parameters.