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====== cufflinks 2.0.0 installation ======
Depends on ''samtools'' and ''boost''!  Make sure those are installed first...

===== Unpack =====
<code>tar zxf cufflinks-2.0.0.tar.gz
cd cufflinks-2.0.0</code>

===== Install Eigen headers =====
As of 2.0.0, cufflinks depends on [[http://eigen.tuxfamily.org|Eigen]] as a compile-time dependency.  Download and unzip the Eigen headers somewhere the compiler can find them:

<code>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</code>

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, compile and install =====
<code>./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</code>

===== Prepare module file =====
Allow users to load support for cufflinks using the module system:
<code>mkdir /export/apps/modules/modulefiles/cufflinks</code>

Create the module file, ///export/apps/modules/modulefiles/cufflinks/2.0.0//:
<file>#%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
}</file>

==== Test module file ====
<code>module load cufflinks/2.0.0</code>