Not able to UPDATE BWA in Centos

Question

[David_emir]

Hi,

I am trying to update BWA in centos but not able to do so,

Program: bwa (alignment via Burrows-Wheeler transformation) Version: 0.5.0 (r1200)

i have tried downloading and setting up the path for bwa-0.7.15 but failed to upgrade it.

The path i have set

#!/bin/bash
    BWA_HOME=/home/Exome_seq/bwa-0.7.15
    PATH=$BWA_HOME:$PATH
    export PATH

Please let me know how to upgrade BWA in my system to the latest version.

Thanks, Ateeq

[Michael]

What happens if you type /home/Exome_seq/bwa-0.7.15/bwa directly? What does which bwa give? This is more of a linux configuration problem. In linux you don't need to install a binary to run it. The above code should be put in your .profile (best option) , .bash_profile or .bashrc in your home. Then log off and on or do a $ . .profile. This is all in case you need the freshest builds, otherwise have the sysadmin use the package system.

[Jean-Karim Heriche]

Which version of CentOS are you using ? At least for CentOS 7, bwa-0.7.12 is available in the epel repository so you can install it with yum (CentOS 6 has bwa-0.7.5)