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--- software:genome_assembly:cufflinks:2.0.0 [2012/06/12 09:11] – aorth
+++ software:genome_assembly:cufflinks:2.0.0 [2012/06/13 08:19] (current) – aorth
@@ Line 7: / Line 7: @@
 ===== Install Eigen headers =====
-As of 2.0.0, cufflinks depends on [[http://eigen.tuxfamily.org|Eigen]].  Copy the Eigen headers somewhere the compiler can find them:
+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 cp -R eigen-eigen-6e7488e20373/Eigen /usr/local/<code>
+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>
@@ Line 21: / Line 24: @@
 <code>mkdir /export/apps/modules/modulefiles/cufflinks</code>
-Create the module file, ///export/apps/modules/modulefiles/cufflinks/1.0.3//:
+Create the module file, ///export/apps/modules/modulefiles/cufflinks/2.0.0//:
 <file>#%Module1.0
 #####################################################################
@@ Line 28: / Line 31: @@
 ## by Alan Orth, a.orth@cgiar.org
 ##
-set version   1.0.3
+set version   2.0.0
 set prefix    /export/apps/cufflinks/${version}
 set exec_prefix   ${prefix}
@@ Line 52: / Line 55: @@
 ==== Test module file ====
-<code>module load cufflinks</code>
+<code>module load cufflinks/2.0.0</code>