TopHat 2.1.1

Basic information

Tested on (Requirements)

  • Dependencies to run TopHat:
    • Bowtie2
    • Intel compiler (C y C++)

Installation

After solving the previously mentioned dependencies, you can proceed with the installation.

  1. Download the latest version of the software (Source code - tar.gz) (ccb.jhu.edu/software/tophat/downloads/tophat-2.1.1.Linux_x86_64.tar.gz):

    tar -zxvf tophat-2.1.1.Linux_x86_64.tar.gz
sudo mkdir -p /share/apps/tophat/2.1.1/gcc-4.4.7/bin
cp tophat-2.1.1.Linux_x86_64/* /share/apps/tophat/2.1.1/gcc-4.4.7/bin

Module

#%Module1.0####################################################################
##
## module load tophat/2.1.1_gcc-4.4.7
##
## /share/apps/modules/tophat/2.1.1_gcc-4.4.7
## Written by Juan Pablo Alcaraz Florez
##

proc ModulesHelp {} {
    global version modroot
    puts stderr "Sets the environment for using tophat 2.1.1\
                \nin the shared directory \
                \n/share/apps/tophat/2.1.1/gcc-4.4.7/\
                \nbuilded with gcc-4.4.7"
}

module-whatis "(Name________) tophat"
module-whatis "(Version_____) 2.1.1"
module-whatis "(Compilers___) gcc-4.4.7"
module-whatis "(System______) x86_64-redhat-linux"
module-whatis "(Libraries___) bowtie2"

# for Tcl script use only
set         topdir        /share/apps/tophat/2.1.1/gcc-4.4.7/
set         version       2.1.1
set         sys           x86_64-redhat-linux

conflict tophat
module load bowtie2/2.3.4.1_intel-18.0.2

prepend-path PATH    $topdir/bin

References

  • Manual dentro del paquete del software

Authors

  • Juan Pablo Alcaraz Flórez