software:genome_assembly:cufflinks:2.0.0
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Table of Contents
cufflinks 2.0.0 installation
Depends on samtools
and boost
! Make sure those are installed first…
Unpack
tar zxf cufflinks-2.0.0.tar.gz cd cufflinks-2.0.0
Install Eigen headers
As of 2.0.0, cufflinks depends on Eigen. Copy the Eigen headers somewhere the compiler can find them:
tar xf 3.0.5.tar.bz2 sudo cp -R eigen-eigen-6e7488e20373/Eigen /usr/local/<code> ===== 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 make sudo make install
Prepare module file
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/1.0.3:
#%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 }
Test module file
module load cufflinks
software/genome_assembly/cufflinks/2.0.0.1339492314.txt.gz · Last modified: 2012/06/12 09:11 by aorth