BLAT 36

Basic information

Installation

  1. To download run:

    $ module load intel/19.0.4
$ wget https://genome-test.gi.ucsc.edu/~kent/src/blatSrc.zip
$ unzip batSrc.zip && cd blatSrc

    To use the Intel’s compiler modify the file inc/common.mk: like this:

    CC=icc
COPT=-O3 -xHost

    Create the makefile’s needed directory ~/bin/x86_64.

    mkdir -p ~/bin/x86_64

    Compile:

    make -j6

    Install:

    $ sudo mkdir -p /share/apps/blat/36/intel/19.0.4/bin

# Make sure that the directory ~/bin/x86_64 has only the BLAT's installation
$ sudo cp -r ~/bin/x86_64/* /share/apps/blat/36/intel/19.0.4/bin

  2. Create and place the needed module file. Create a file with the following content:

    36_intel-19.0.4
    #%Module1.0#####################################################################
##
## modulefile blat/36_intel-19.0.4 
##
## /share/apps/modules/blat/36_intel-19.0.4
## Written by Hamilton Tobon Mosquera.
proc ModulesHelp { } {
     global version modroot
     puts stderr "Sets the environment for using blat 36\
     \nin the shared directory /share/apps/blat/36/intel/19.0.4\
     \nbuilt with Intel 19.0.4."
}    

module-whatis "(Name________) blat"
module-whatis "(Version_____) 36"
module-whatis "(Compilers___) Intel 19.0.4"
module-whatis "(System______) x86_64-redhat-linux"
module-whatis "(Libraries___) "

conflict blat

# for Tcl script use only
set     topdir       /share/apps/blat/36/intel/19.0.4
set     version      36
set     sys          x86_64-redhat-linux

prepend-path   PATH            $topdir/bin

    Create the needed folder and place it:

    $ sudo mkdir /share/apps/modules/blat
$ sudo mv 36_intel-19.0.4 /share/apps/modules/blat/

Authors