Question: Not able to UPDATE BWA in Centos
0
gravatar for David_emir
2.5 years ago by
David_emir310
India
David_emir310 wrote:

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

bwa new version • 968 views
ADD COMMENTlink written 2.5 years ago by David_emir310

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.

ADD REPLYlink modified 2.5 years ago • written 2.5 years ago by Michael Dondrup45k

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)

ADD REPLYlink written 2.5 years ago by Jean-Karim Heriche18k
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