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

tar zxf cufflinks-2.0.0.tar.gz
cd cufflinks-2.0.0

As of 2.0.0, cufflinks depends on Eigen as a compile-time dependency. Download and unzip the Eigen headers somewhere the compiler can find them:

tar xf 3.0.5.tar.bz2
sudo mkdir -p /export/apps/eigen/3.0.5/include
sudo cp -R eigen-eigen-6e7488e20373/Eigen /export/apps/eigen/3.0.5/include

The configure/make scripts expect Eigen's headers to live somewhere in a folder called "include". Don't fight it, just put them somewhere (even /usr/local/include would work) where the compiler can find them. I'll use /export/apps because it's neater.

./configure --prefix=/export/apps/cufflinks/2.0.0 --with-boost=/export/apps/boost/1.47.0 --with-bam=/export/apps/samtools/0.1.18 --with-eigen=/export/apps/eigen/3.0.5
make -j4
sudo make install

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

mkdir /export/apps/modules/modulefiles/cufflinks

Create the module file, /export/apps/modules/modulefiles/cufflinks/2.0.0:

#%Module1.0
#####################################################################
##
## cufflinks Modulefile
## by Alan Orth, a.orth@cgiar.org
##
set version   2.0.0
set prefix    /export/apps/cufflinks/${version}
set exec_prefix   ${prefix}
set url "http://cufflinks.cbcb.umd.edu/"
set msg "This module adds cufflinks v$version to various paths\n\ncufflinks Official Site: $url\n"

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

module-whatis   "$msg"

conflict      cufflinks

prepend-path  PATH    ${exec_prefix}/bin
# cufflinks 1.0.3 was compiled against boost 1.47.0, make sure if can find boost!
prepend-path  LD_LIBRARY_PATH /export/apps/boost/1.47.0/lib

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

module load cufflinks/2.0.0