Hello,

I had this error when trying to install cufflinks and it seems like a common error when I search around but I'm still not sure how to fix it. None of the methods I have found have worked for me. I installed samtools in folder and provided the path to that folder with the --with-bam option but it still says its cannot locate it?

ubuntu@ip-172-31-19-217:~/software/cufflinks-2.2.1$ ./configure --with-boost=/home/ubuntu/software/boost --with-bam=/home/ubuntu/software/samtools-1.4.1/samtools
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for gawk... gawk
checking whether make sets $(MAKE)... yes
checking for gawk... (cached) gawk
checking for g++... g++
checking for C++ compiler default output file name... a.out
checking whether the C++ compiler works... yes
checking whether we are cross compiling... no
checking for suffix of executables...
checking for suffix of object files... o
checking whether we are using the GNU C++ compiler... yes
checking whether g++ accepts -g... yes
checking for style of include used by make... GNU
checking dependency style of g++... gcc3
checking for gcc... gcc
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking dependency style of gcc... gcc3
checking whether make sets $(MAKE)... (cached) yes
checking for ranlib... ranlib
checking for a BSD-compatible install... /usr/bin/install -c
checking for a Python interpreter with version >= 2.4... python
checking for python... /usr/bin/python
checking for python version... 2.7
checking for python platform... linux2
checking for python script directory... ${prefix}/lib/python2.7/site-packages
checking for python extension module directory... ${exec_prefix}/lib/python2.7/site-packages
checking for boostlib >= 1.47.0... yes
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 <bam version.hpp="">. See http://randspringer.de/bam for more documentation.