Unable to detect bamlib libraries (version or higher) when installing cufflinks

If you are installing Cufflinks according to the instructions as given by http://cufflinks.cbcb.umd.edu/tutorial.html. 

The compiling of the components below are quite expected.
boost,
eigen,
samtools

But when finally compiling cufflinks, you might encounter errors

.....
..... 
checking for bamlib... configure: error: We could not detect the bam libraries 
(version    or higher). If you have a staged bam library (still not installed) 
please specify $BAM_ROOT in your environment and do not give a PATH to --with-bam option.  
If you are sure you have bam installed, then check your version number looking in......... 
See http://randspringer.de/bam for more documentation. 

The source of the error is somehow the cufflinks is not able to find the libraires and binaries found by samtools. This is especially true if you compiled the components into distinct directories and not into standard directories like /usr/local/bin and /usr/local/lib /usr/local/include

To ensure that the cufflinks detects the samtools libraries, you might want to do the following.

# mkdir -p /usr/local/include/bam
# cp ${SAMTOOLS}/libbam.a /usr/local/lib/
# cp ${SAMTOOLS}/*.h /usr/local/include/bam
# cp ${SAMTOOLS}/samtools /usr/local/bin/

Try compiling again. It should work