Depends on samtools and boost! Make sure those are installed first…

tar zxf tophat-2.0.3.tar.gz
cd tophat-2.0.3

./configure --prefix=/export/apps/tophat/2.0.3 --with-boost=/export/apps/boost/1.47.0 --with-bam=/export/apps/samtools/0.1.18
make
sudo make install

Allow users to load support for tophat using the module system:

sudo mkdir -p /export/apps/modules/modulefiles/tophat

Create the module file, /export/apps/modules/modulefiles/tophat/2.0.3:

#%Module1.0
#####################################################################
##
## tophat Modulefile
## by Alan Orth, <a.orth@cgiar.org>
## June 13, 2012
##
set version   2.0.3
set appname   tophat
set prefix    /export/apps/${appname}/${version}
set exec_prefix   ${prefix}/bin
set datarootdir   ${prefix}/share
set url "http://tophat.cbcb.umd.edu"
set msg "This module adds tophat v$version to various paths\n\ntophat Official Site: $url\n"

proc ModulesHelp { } { 
  puts stderr "$msg"
}

module-whatis   "$msg"

conflict tophat

prepend-path  PATH    ${exec_prefix}
prepend-path  MANPATH   ${datarootdir}/man

# tophat depends on samtools, load the samtools module as well
if { ![is-loaded samtools] } { 
    module load samtools
}

# tophat depends on bowtie, load the bowtie module as well
if { ![is-loaded bowtie] } { 
    module load bowtie
}

module load tophat/2.0.3