Installation by Pip

This guide will walk you through the steps for installing MuscleX using pip, Python’s package manager.

Before You Begin

This installation guide assumes that you have already set up a virtual environment according to our Prerequisite Guide: Setting Up Virtual Environments. It is essential to have your environment ready to ensure MuscleX is installed in an isolated space, preventing any potential conflicts with other packages on your system.

If you have not yet prepared a virtual environment, please refer to the prerequisite guide for detailed instructions.

Installing MuscleX

With your virtual environment set up and activated, you are now ready to install MuscleX. Execute the following command within your virtual environment:

pip install --upgrade musclex

Or, to install the most current development version directly from GitHub:

pip install --upgrade git+https://github.com/biocatiit/musclex.git

Ensure that these commands are run within the virtual environment you have prepared for MuscleX to maintain the isolation from other Python packages.

Post-Installation

After successfully installing MuscleX, you can verify the installation by checking the installed packages in your environment:

pip list | grep musclex

This command should list MuscleX and its version, indicating that the installation was successful.

Running MuscleX

With MuscleX installed, you can now run the application directly from the command line, within your virtual environment. Make sure your virtual environment is activated whenever you wish to use MuscleX.

To deactivate your virtual environment when you’re finished working with MuscleX, simply run:

deactivate

if you are using a venv environment, or:

conda deactivate

if you are using a Conda virtual environment.

Updating MuscleX

To update MuscleX to the latest version, use the following command within your virtual environment:

pip install --upgrade musclex

System install (Only recommended for Linux and Mac OS users)

Instead of a virtual environment install you may install the program directly on the system. It is not recommended as it may create conflicts with other libraries on your computer, or other versions of MuscleX already installed.

Run this command to install Muscle X programs

pip install musclex

Note: If you are upgrading, add –upgrade at the end.

Running a program

If you installed MuscleX in a virtual environment on Linux or Mac OS

To run a program, you need to activate the virtual environment first. Assuming you created a virtual environment called musclex, you can activate it by typing the following command in the terminal:

conda activate musclex # or use 'source activate musclex' if you are using a venv environment

Then you can run the program by typing the program shortcut in the terminal.

Simply run

musclex [program shortcut]

For example, run this command to run Diffraction-Centroids

musclex dc

If you get ImportError: C extension: iNaT not built. If you want to import pandas from the source directory, you may need to run ‘python setup.py build_ext –inplace –force’ to build the C extensions first while you’re running the program, please re-install pandas by

pip install -U pandas

If you get “Could not load the Qt platform plugin”, it might be because you have the normal version of OpenCV already installed. Try to remove it with:

pip uninstall opencv-python
pip install --upgrade opencv-python-headless

If this change does not work, install an older version of OpenCV by

pip install opencv-python==4.2.0.32

Once you are done using MuscleX, you can deactivate the virtual environment by typing the following command in the terminal:

conda deactivate # or use 'deactivate' if you are using a venv environment

If you installed MuscleX in a virtual environment on Windows

To run a program, you need to activate the virtual environment first. Assuming you created a virtual environment called musclex, you can activate it by typing the following command in the anaconda prompt terminal:

conda activate musclex # or use 'activate musclex' if you are using a venv environment

Then you can run the program by typing the program shortcut in the anaconda prompt terminal.

Simply run

musclex [program shortcut]

For example, run this command to run Diffraction-Centroids

musclex dc

Once you are done using MuscleX, you can deactivate the virtual environment by typing the following command in the anaconda prompt terminal:

conda deactivate # or use 'deactivate' if you are using a venv environment

Updating

pip install -U musclex

if you do not need to update other dependencies, you can run

pip install -U --no-deps musclex

if you need to install the latest version directly from github, you can run

pip install git+https://github.com/biocatiit/musclex.git

if you need to install a previous version (e.g. v1.15.2) directly from github, you can run

pip install git+https://github.com/biocatiit/musclex.git@v1.15.2

Troubleshooting

If you encounter any issues during the installation process, ensure that your virtual environment is correctly set up and activated. For further assistance, refer back to the Prerequisite Guide: Setting Up Virtual Environments or consult the troubleshooting section of the MuscleX documentation.