Install SRA toolkit

SRA toolkit contains important tools to manipulate SRA (Short Read Archive) file.

The objective of this article is to show you, how to install SRA toolkit on Ubuntu/Linux system.


Installation



1. Download the last version for your computer operating system from here

Use the following command on Linux to download the file sratoolkit.2.4.1-ubuntu64.tar.gz:

Code BASH :
 
#Download the file for ubuntu system
wget http://ftp-trace.ncbi.nlm.nih.gov/sra/sdk/2.4.1/sratoolkit.2.4.1-ubuntu64.tar.gz
# Unzip the archive
tar xzvf sratoolkit.2.4.1-ubuntu64.tar.gz
 



2. Modify your .bashrc file so that when you type "fastq-dump" , for example, it calls the program:
Code BASH :
export PATH=$PATH:/directory/sratoolkit.2.4.1-ubuntu64/bin 



Directory is equal to the directory that you have installed sratoolkit in. Example:
Code BASH :
export PATH=$PATH:/home/kassambara/Documents/sequencing/tools/sratoolkit.2.4.1-ubuntu64/bin 


Enjoyed this article? I’d be very grateful if you’d help it spread by emailing it to a friend, or sharing it on Twitter, Facebook or Linked In.

Show me some love with the like buttons below... Thank you and please don't forget to share and comment below!!
Avez vous aimé cet article? Je vous serais très reconnaissant si vous aidiez à sa diffusion en l'envoyant par courriel à un ami ou en le partageant sur Twitter, Facebook ou Linked In.

Montrez-moi un peu d'amour avec les like ci-dessous ... Merci et n'oubliez pas, s'il vous plaît, de partager et de commenter ci-dessous!





This page has been seen 51111 times