BLAST+ Tutorial - Preparing the HPC Environment

Introduction

Before starting with the tutorial, we first need to prepare our environment.

Please note that the instructions assume that the UFS HPC is being used to complete the tutorial. However, it is possible to complete the tutorial on a local Linux machine if the BLAST+ tools are installed and available on the system. In this scenario, ignore the instructions relating to the UFS HPC.

Getting Started

To prepare for the tutorial, perform the following steps:

1. Login to the UFS HPC

2. You should now be in your home directory. Now create a directory named blast_tutorial

3. Move into blast_tutorial and download the necessary data files that will be used in the tutorial using wget:

   $ wget  https://docs.hpc.ufs.ac.za/training/blast_tutorial/files/VFDB_setB_nt.fas.gz
   $ wget  https://docs.hpc.ufs.ac.za/training/blast_tutorial/files/query.faa
   

4. Start an interactive job (qwiz) with the following parameters (See Howto submit jobs using PBS):

   • Resources Required = gen5
   • Nodes = 1
   • Cores = 4
   • Memory = 8
     
     

5. Ensure that the bioinformatics container is loaded:

   $ module load bioinformatics
   

6. Activate the container:

   $ $runc
   

7. Make sure you have access to the blast+ tools:

   $ blastn -h
   

   You should see the blastn help documentation displayed.

Our environment is now set up for BLAST off!