How to update existing Samtools

[Muthukumar]

Hi all ,

Since I am new to RNA seq as well as Linux. I don't how to update existing sam tool version to current updated version in wesite. Can u help me to tell the ways to do it in ubuntu terminal.

[GenoMax]

Do you have administrator privileges on this machine? Otherwise you may need to "make" and run samtools from a directory you own.

[Muthukumar]

Do you have administrator privileges on this machine? Otherwise you may need to "make" and run samtools from a directory you own.

Thanks for reply. I do have an administrator privilege. Thing is that sam tools already in usr\bin. I mean older version . My question is whether i have to remove sam tools from there and install new version from website or any other option to update the existing tool.

[GenoMax]

If you have admin privileges then you could save the version that is currently in /usr/bin to something like

$ cp -pi /usr/bin/samtools /usr/bin/samtools_old (or append version #)

Then do the install with make prefix set to /usr/bin. Su to root account when you install.

Note: I am assuming that you are the only (or major) user on this system. When you are changing the default samtools available on the system (and there are others who use this machine) then you should let other users know BEFORE you make this change.

[mbblack]

Thanks for reply. I do have an administrator privilege. Thing is that sam tools already in usr\bin. I mean older version . My question is whether i have to remove sam tools from there and install new version from website or any other option to update the existing tool.

What flavor of Linux are you running? You may be able to simply use your system's package manager to do this.

For example, with CentOS 7 and epel repository installed, a simple:

sudo yum update samtools.x86_64

and you're done.

[Muthukumar]

Thanks for valuable reply