compiling of cufflinks failed due to bamlib error

[kristianunger]

Hi there,

I know this issue has been addressed already in the instructions and also in some other forums. However, since I don't get it resolved after spending loads of time I hope someone can help me sorting out my problem:

I am trying to compile the latest version of cufflinks (2.2.1) according to instructions given here http://cole-trapnell-lab.github.io/c...tting_started/ but I end up with the error

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.

From the instructions and having a look into the configure file I understand that in the first place the standard location /usr/local is searched for the samtools files which have to be organised as follows


/usr/local/include/bam #has to contain the header files *.h
/usr/local/lib #has to contain libbam.a

and the samtools binary needs to go somewhere in $PATH .

Since I only can do local installations I generated a folder in my home /home/group/user/:

/home/group/user/bin/samtools

and set up the structure described above:

/home/group/user/bin/samtools
/home/group/user/bin/samtools/lib containing the libbam.a file
/home/group/user/bin/samtools/include/bam containing all the header files

then added the directory to PATH by:

export PATH=$PATH:/home/group/user/bin/samtools

and executed configure using

./configure --prefix=/home/group/user/cufflinks/src/ --with-eigen=/home/group/user/Eigen/

and get the following output:

bash-4.2$ ./configure --prefix=/home/group/user/cufflinks/src/ --with-eigen=/home/group/user/Eigen/
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 ANSI C... 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}/lib64/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.

I really tried everything suggested in the forums such setting the BAM_ROOT variable but I cannot work out what the problem is!

Can you please help? I am sure there is something stupid I am missing and and blind for after countless times of trying...

Many thanks!

Kristian

[jgrant@smith.edu]

I am having the same issues, installing at root, even after following instructions I found for dealing with the problem. I also tried installing with homebrew and got the same error:

==> ./configure --prefix=/usr/local/Cellar/cufflinks/2.2.1 --mandir=/usr/local/Cellar/cufflinks/2.2.
checking for python platform... darwin
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.

Any help would be hugely appreciated!

[sklages]

Installing current samtools already results in a "correct" directory structure with 'include', 'lib' etc.

1) put samtools in bin or install current samtools and export path to

export /path/to/samtools/bin:$PATH

2) configure, pointing to lib dir,

export CPPFLAGS="-I/path/to/eigen/include/eigen3"

./configure --prefix=/path/to/cufflinks/2.2.1 --with-boost=/path/to/boost --with-bam=/path/to/samtools/lib --with-eigen=/path/to/eigen

[...]
checking for boostlib >= 1.47.0... yes
checking for bamlib... yes
checking for eigenlib... yes
[...]

This should at least make configure work ...

best,
Sven

[ohmiyajohn]

Furthermore, you need an additional step.
You need to copy version.h to version.hpp.

$ cp /to/path/samtools/include/bam/version.h /to/path/samtools/include/bam/version.hpp

My issue is sorted out by the above procedure.