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--- software:genome_assembly:cufflinks:2.0.0 [2012/06/12 08:52] – created aorth
+++ software:genome_assembly:cufflinks:2.0.0 [2012/06/13 08:16] – [Configure, compile and install] aorth
@@ Line 5: / Line 5: @@
 <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
+<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
+make -j4
 sudo make install</code>
 ===== Prepare module file =====
 Allow users to load support for cufflinks using the module system: