Connect with us

Docking

Installing GalaxyPepDock & Galaxy-Server on Ubuntu

Published

on

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 CEO 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.

Docking

What values are considered as good or bad in computational docking?

Published

on

After performing computational docking, a question that comes to mind most is “what docking score is considered good or bad”. In this article, we will discuss this in detail. (more…)

Continue Reading

Bioinformatics Programming

How to sort binding affinities based on a cutoff using vs_analysis.py script?

Published

on

How to sort binding affinities based on a cutoff using vs_analysis.py script?

Previously, we have provided a Python script (vs_analysis.py) to analyze the virtual screening (VS) results of Autodock Vina. Now, we have updated this script to sort binding affinities based on user inputted cutoff value. (more…)

Continue Reading

Docking

Virtual Screening using Autodock Vina: Frequently Asked Questions & Answers for Starters

Published

on

Virtual Screening using Autodock Vina: Virtual Screening: Frequently Asked Questions & Answers for Starters

Virtual Screening (VS) is one of the important techniques in bioinformatics. It can be easily performed using Autodock Vina. We have provided detailed articles on this topic. In this article, we are trying to answer some FAQs for beginners. (more…)

Continue Reading

LATEST ISSUE

ADVERT