How To Install Sequence Aligners: Blat Gsmapper

Question

[HG]

Hi everyone i need to install Sequence aligners: BLAT GSMapper to run GAA(https://github.com/ghyao/GAA), can anyone help me out how to install BLAT through command line. I am using unbuntu 12.4

Thank you advance.

Answer 1

[Kashyap Chhatbar]

Install blat through command line:

You might want to go here http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/blat/

Since you have mentioned that your operating system is Ubuntu 12.4, I suppose this would work. Download the blat file from the list and make it executable by changing permission. If you want it for other platform, follow this link http://hgdownload.cse.ucsc.edu/admin/exe/ and select whichever platform appropriate

chmod +x blat

and you can put that into your bin folder if you have added it to your path or you can execute it directly from that directory itself using this command

./blat