Building UCSC short-sequence alignment tool - BLAT

BLAT executable

If you are running 64bit Linux like system, you can download BLAT executable directly from UCSC directory and use it:

single BLAT executable for 64 bit system:

http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/blat/

"BLAT suit" contains list of tools:
http://genome-test.cse.ucsc.edu/~kent/exe/linux/

use "ln"command to create dynamic link to execute BLAT anywhere:

$ ln -s /absolute/path/of/downloaded/blat /usr/local/bin

Build BLAT from source

To build from source code, look at this list for latest version of BLAT:
http://users.soe.ucsc.edu/~kent/src/

Then:

1. check shell environment. 

 It should contain a MACHTYPE variable.  Typical values, for example: i386 i686 sparc alpha x86_64 ppc If there is none, set it to indicate your CPU architecture for example, 

$ MACHTYPE=i686$ export MACHTYPE

You need to do this if your existing MACHTYPE is a long string such as: i686-pc-linux-gnu since this is used as an argument on the command line to gccwhich will not work with the - signs in the strings. Typical values: i386 i686 x86_64 sparc ppc To determine the machine cpu type of your computer, try one of these uname command options:

$ uname -m  $ uname -p  $ uname -a

Remember to set this MACHTYPE in your .bashrc or .tcshrc home directory environment files so it will be set properly at your next login.

2. Create a directory

where binaries will be moved to during the build of the source tree:

$ mkdir -p ~/bin/${MACHTYPE}

3. Build the tool

go into uzipped BLAT directory, and run:

$ make

Note: there is no need to do this as 'root'.

4. Find the tool and make it executable anywhere:

$ cd ~/bin/$MACHTYPE 

(it's usually under current home directory / user name / bin /$ MACHTYPE)

and then use "ln" command to make it executable anywhere. e.g. 

$ ln -s /home/chris/bin/i686/blat /usr/local/bin/blat