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🐍 Toehold Switch Creator Wiki 🧬

About the requirements

The Toehold Switch Creator software is written in the Python language. So that they can run critical parts of the code, several libraries need to be downloaded. In this case, anaconda should be used as package manager, this tool is downloaded directly from the terminal of Linux or Mac depending yout case.

One of the benefits of anaconda is that it allows the creation of programming environments. Which are folders in which we can configure, through terminal, Python-specific packages, or different versions of Python (or Python any programming language), so if we make a mistake when performing the installation of a package or a language, it is enough that we generate another environment of programming (and if we want) let's delete the one that is broken

The software to be installed is the following:

1. Anaconda
2. Bioconda
3. Python 3.7.x
4. ViennaRNA
5. PrimedRPA
6. Openpyxl

🐧 Linux / 🌊 Windows

The necessary software tools can only be run on a MacOS or Linux system. In case of having a computer with Windows 10, it is necessary to install the Windows Subsystem for Linux 2 (WSL 2). This subsystem consists of a Linux terminal installed in Windows 10, under which the code scripts and bioinformatics packages to be used can be executed, you can find a guide to install said subsystem in the following link.

Anaconda

The installation of anaconda will vary depending on whether the operating system is pure Linux or a subsystem of this, in the case of the latter you can go to corroborate the installation process of anaconda in the same link that we described previously

Bioconda

To use GUI packages with Debian Linux, you will need to install the following extended dependencies for Qt:

apt-get install libgl1-mesa-glx libegl1-mesa libxrandr2 libxrandr2 libxss1 libxcursor1 libxcomposite1 libasound2 libxi6 libxtst6

After this you must open a terminal and run the following:

sha256sum /path/filename

To install Anaconda for Python 3.7 enter the following

bash ~/Downloads/Anaconda3-2020.02-Linux-x86_64.sh

Python 3.7.x

Now we proceed to install Anaconda for Python 3.7.x

conda install python=3.7

ViennaRNA

For the installation of ViennaRNA you may run the following commands on your terminal

conda install -c bioconda viennarna

PrimedRPA

Now for the the installation of PrimedRPA you may run the following commands on your terminal

conda install -c bioconda primedrpa

Openpyxl

Finally for the installation of Openpyxl you may run the following commands

conda install xlswriter

Run Toehold Switch Creator

Once you have installed all the software dependencies, you can run Toehold Switch Creator with the following command. Remember to run it on the same directory you have all your input files.

python TH_Creator.py

🍎 MacOS

Python 3.7.x

Make sure you have the latest version of Python. For that, go to your terminal and type:

python --version

If you don't have the latest Python version you can follow this tutorial for installation.

Anaconda

You can install Anaconda using either the graphical installer or the command-line instructions. The steps to follow are provided in the following documentation. Alternatively, you can also install Miniconda which is a free minimal installer for conda. Detailed instructions for installing Miniconda are in the following link.

Bioconda

After installing your conda environment (either Anaconda or Miniconda) you will need to add the following channels to set up Bioconda. It's very important to add them in the following order:

conda config --add channels defaults
conda config --add channels bioconda
conda config --add channels conda-forge

For any further documentation on Bioconda revise the following link.

PrimedRPA

You can install PrimedRPA using the following command:

conda install -c bioconda primedrpa

Further documentation on PrimedRPA and how to use it can be found on its GitHub repository.

ViennaRNA

Install ViennaRNA on your conda environment using the following command:

conda install -c bioconda viennarna

Openpyxl

Finally for the installation of Openpyxl you may run the following command:

conda install xlswriter

Run Toehold Switch Creator

Once you have installed all the software dependencies, you can run Toehold Switch Creator with the following command. Remember to run it on the same directory you have all your input files.

python TH_Creator.py