python logo

Installation by Pip¶

In order to install the program, you need to install python 2.7 or 3.6.

Preparing¶

There are some modules need to be installed before installing Muscle X. They are Pip, OpenCV, PyQT4 or PyQT5, gfortran, PyFAI and Cython.

Linux¶

sudo apt-get update
sudo apt-get install python-pip libjpeg-dev libopencv-dev python-opencv python-qt4 cython pyfai gfortran

Mac OS¶

/usr/bin/ruby -e "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/master/install)"
brew install opencv
brew install cartr/qt4/pyqt
brew install gcc
sudo easy_install pip
sudo pip install pyfai
sudo pip install cython

Windows¶

For windows, we have built the Fortran source for you, so Fortran compiler is not required. But C compiler is still required to build C extensions during the installation process, and Microsoft Visual C++ (MSVC) is recommended.

Python 2.7 on Windows¶

The default MSVC chosen by Python 2.7 is MSVC 9.0. We recommend forcing the use of MSVC 14.0 instead. Follow the steps below.

Uninstall Microsoft Visual C++ Compiler for Python 2.7 (MSVC 9.0) If Microsoft Visual C++ Compiler for Python 2.7 is installed, uninstall it (See Repair or remove programs in Windows 10).
Install Microsoft Build Tools 2015 Update 3 (MSVC 14.0) The minimal customized installation of Microsoft Build Tools 2015 Update 3 is not enough. Make sure Windows SDK (8.1 or 10) is included.
Temporarily set environment variable VS90COMNTOOLS Type the following command in your current cmd prompt: set VS90COMNTOOLS=%VS140COMNTOOLS%

Then install dependencies:

pip install numpy cython python-qt5 opencv-python pyfai

Python 3.6 on Windows¶

The default MSVC chosen by Python 3.6 is MSVC 14.0. The minimal customized installation of Microsoft Build Tools 2015 Update 3 is enough. Then install dependencies:

pip install cython numpy pyqt5 opencv-python pyfai

Note

Omit keyword sudo in the commands in following parts when working on Windows.

Installing¶

System install¶

Run this command to install Muscle X programs

sudo pip install musclex

Virtual environment install¶

Instead of a system install you may install inside a virtual environment. A virtual environment allows you to have a clean environment that is independent of othe software installations. Use the following to create a virtual environment and install musclex inside it:

python3 -m pip install --user virtualenv
python3 -m venv musclex
source musclex/bin/activate
which python3
pip install --upgrade pip
pip3 install pyopencl
pip3 install cython
pip3 install numpy
pip3 install opencv-python
pip3 install pyfai==0.15.0
pip3 install PyQt5
pip3 install musclex
#pip3 install git+https://github.com/biocatiit/musclex.git # use this for the most up-to-date version
musclex eq

To exit the virtual environment use:

deactivate

To re-enter the virtual environment use:

source musclex/bin/activate
musclex eq

Running a program¶

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

Updating¶

sudo pip install -U musclex

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

sudo 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