MassDash Installation on MacOS Big Sur

This guide will help you install MassDash on MacOS Big Sur.

Note

This tutorial was created using a clean installation of MacOS Big Sur using a virtual machine. The virtual machine was created using Oracle VM VirtualBox, with 32Gb of RAM, 8 processors, and 64Gb of storage. The virtual machine was created using the macOS Big Sur iso file from The Internet Archive.

Prerequisites

It is recommended to use Anaconda to manage Python environments and packages. You can download Anaconda from here. You can find documentation for installing Anaconda on MacOS here.

Installation

  1. Launch a terminal and create a new conda environment using the following command:

    conda create -n massdash python=3.9 -y
Create a new conda environment

  1. Activate the new conda environment using the following command:

    conda activate massdash
Activate the new conda environment

  1. Install massdash using the following command:

    pip install massdash
Install massdash

Usage

Help

You can get help on how to use MassDash’s GUI by running the following command in the terminal:

massdash gui --help
../_images/macos_conda_cmd_massdash_gui_help.png

Launch MassDash GUI

You can launch MassDash’s GUI by running the following command in the terminal:

massdash gui

A browser window will open with the MassDash GUI. If the browser window does not open, you can navigate to the following URL in your browser using the local url provided in the Anaconda CMD.exe output, by default it should be http://localhost:8501/, unless the port is changed.

Note

It is recommended to use Google Chrome or Firefox to open the MassDash GUI instead of Safari.

Note

MassDash warns you that onnxruntime, torch, and torchmeets are not installed. You can ignore this warning if you do not plan to use the MassDash’s peak picking conformer model.

../_images/macos_conda_cmd_massdash_gui_run.png

Once the browser window opens, you can start using MassDash’s GUI to visualize your mass spectrometry data. For more information on the GUI, please refer to the MassDash GUI Documentation.

../_images/macos_massdash_gui.png ../_images/macos_massdash_gui_example.png