mutatex/INSTALL at master · ELELAB/mutatex · GitHub

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INSTALLATION
============

Requirements
------------

MutateX is designed to run on Linux and MacOS.

Notice that, while MutateX runs on the Windows Subsystem for Linux,
its parallelization strategy has been reported not to run correctly (see Issue #205).
We recommend running MutateX with only one process when running on WSL, or to use a
full Linux virtual machine, or just a Linux system altogether.

MutateX requires Python >=3.10 and the following Python packages:

setuptools
biopython
numpy
matplotlib
scipy
six
openpyxl
pandas
logomaker
pyyaml
adjustText >= 0.8

The most convenient way to install MutateX is by creating a Python virtual
environment in which all the requirements will be installed. In order to do
this, you should have the virtualenv and pip packages installed in your system
as well.

MutateX also requires a version of FoldX to be present on your system. Please
refer to http://foldxsuite.crg.eu to obtain one.

Installation steps
------------------

1) if you have git, download the git codebase or clone the repository:

	git clone https://github.com/ELELAB/mutatex.git

2) First create the virtual environment using the virtualenv package and
activate it:

	virtualenv mutatex-env
	. mutatex-env/bin/activate

3) install mutatex using the included setup file. All the requirements will
will be automatically installed

	cd mutatex
	python setup.py install

4) The mutatex scripts should now be available to run

5) This step is optional, but strongly advised. MutateX needs to know the
location of the FoldX binary and rotabase.txt file in order to work. Depending
on the version you are using, you might need to provide the binary file only.
MutateX first tries to find these files looking at the content of the FOLDX_BINARY
and FOLDX_ROTABASE system variables. Therefore, it is advisable to set these
system variables in the .profile or .bashrc file in your user's home, by adding
the following lines:

	export FOLDX_BINARY=/usr/local/foldx/foldx
	export FOLDX_ROTABASE=/usr/local/foldx/rotabase.txt

alternatively, the user can provide the location of such files directly on the
command line of the mutatex script.