how to install samtools

Question

[Chenglin]

I need to install samtools. I saw the instruction on the webpage (http://www.htslib.org/download/) but did not get it.

cd samtools-1.x    # and similarly for bcftools and htslib
make

make prefix=/where/to/install install

What does make prefix=/where/to/install install this mean? Do I need substitute "/where/to/install" with a real path and keep prefix and install?

If so, what is the real path for? Any help, please? Thanks!

Chenglin

[Charles Plessy]

If you are using a Linux system based on Debian (like Debian itself, Ubuntu, MInt, ...) then you can also install samtools with your system's package management tool. (From the command line: apt-get install samtools).

Answer 1

[GenoMax]

Real path is a directory on your computer where you want to install samtools. If that directory is /usr/local/bin then you would add make prefix=/usr/local/bin install when you "make".

[Chenglin]

Thank you very much for your answer. Can you please explain what is the command make prefix=/where/to/install install for? I appreciate very much.

[GenoMax]

prefix determines the directory where the executable will be installed. Make is a utility that is used to automatically build programs from source code.

[Chenglin]

Thank you very much! Do you think it will be a problem if I don't do the second command (make prefix=/usr/local/bin install)?

[GenoMax]

If you don't do that command (and you won't be able to if you don't have root privileges on this machine) then you would either need to run samtools by providing full path to the executable or you would need to add the directory containing samtools executables to $PATH.