BLAT Installation and run

Question

[Bioinfonext]

I am not able to understand how to run blat.

I downloaded source and executables files: https://users.soe.ucsc.edu/~kent/src/blatSrc.zip and http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/.

what is the role of executables file here?

Thanks Yogesh

Answer 1

[Michael]

Hi Yogesh,

the role of having the executables is that you don't have to compile them from source, which might be difficult. If you have linux or macos, you just download the executable and run it in a terminal.

[Bioinfonext]

Hi Michael

Thanks for reply. I got your point. I unzip blat at this location: /home/yog/software/blatSrc/

So at what location should I download executable file and after downloading, if I type ./blat, will it work?

[Michael]

On UNIX like systems it does normally not matter where you put the executable, just download the compatible binary and type /path/to/blat. I have a bin directory in my home also to put binaries for local use, but that is up to you. As to whether it is going to work or not, that depends on the compatibility between your OS and the binary, on Linux, I'd say "likely", MacOS "most likely" , Windows "most likely not" unless you have Windows 10 with ELF support. The easiest way is to simply try it out :)

[GenoMax]

You don't need to get both both source (blatSrc) and executables. In this case just getting the executables is what you need to do. Based on the directory name above you may have downloaded source files and not the executable.