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