GalaxyPepDock is a software used for protein-peptide docking based on interaction similarity. In this article, we will install GalaxyPepDock on Ubuntu.

Getting started

Let’s update and upgrade the system first.

$ sudo apt-get update

$ sudo apt-get upgrade

Remember Galaxy requires Python 3.5 or 3.6. Check your Python version python --version. If required download or upgrade your python as shown below.

$ sudo apt-get install python3.6

$ sudo apt-get install python3.7

Downloading GalaxyPepDock

We will download GalaxyPepDock from Github.

Open a terminal (Ctrl+Alt+T) and change to the directory where you want to download the software. Let’s say Downloads and type the following command on the terminal:

$ cd Downloads/

$ wget https://github.com/seoklab/GalaxyPepDock/archive/master.zip

If you want to download it manually, then click here.

Installing GalaxyPepDock

Now, type the following commands from the same directory.

$ unzip master.zip

$ cd GalaxyPepDock-master/

$ ./install.sh

After installation completes, set environment variables.

$ sudo gedit ~/.bashrc

The file will open in an editor. Go to the end of the file and paste the following line. Remember to replace the ‘user’ with your username.

$ export GALAXY_HOME=/home/user/Downloads/GalaxyPepDock-master/

Now save it (Ctrl+S) and close. Go back to the terminal and type the following command.

$ source ~/.bashrc

Now, you have installed GalaxyPepDock on your system. You can run it by typing a complete path to the GalaxyPepDock.

Downloading Galaxy Server

$ cd Downloads/

$ wget https://github.com/galaxyproject/galaxy/archive/master.tar.gz

Installing Galaxy Server

Now, type the following commands from the same directory.

$ tar xvzf master.tar.gz

$ cd galaxy-master/

$ sh run.sh

It will take some time to finish. After that, you will be able to view Galaxy in your browser at http://localhost:8080