====== cufflinks 1.0.3 installation ======
Depends on ''samtools'' and ''boost''!  Make sure those are installed first...

===== Unpack =====
<code>tar zxf cufflinks-1.0.3.tar.gz
cd cufflinks-1.0.3</code>

===== Configure, compile and install =====
<code>./configure --prefix=/export/apps/cufflinks/1.0.3 --with-boost=/export/apps/boost/1.47.0 --with-bam=/export/apps/samtools/0.1.17
make
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/1.0.3//:
<file>#%Module1.0
#####################################################################
##
## cufflinks Modulefile
## by Alan Orth, a.orth@cgiar.org
##
set version   1.0.3
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</code>