Installing GalaxyPepDock & Galaxy-Server on Ubuntu

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2 mins read
Installing galaxy on Ubuntu

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

Tariq is founder of Bioinformatics Review and a professional Software Developer at IQL Technologies. His areas of expertise include algorithm design, phylogenetics, MicroArray, Plant Systematics, and genome data analysis. If you have questions, reach out to him via his homepage.

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