install cufflinks-2.1.1

[yueli]

Hi,

I try to install cufflinks-2.1.1.

./configure

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.


Anything I can do?

Thanks!

[GenoMax]

See the section on "installing samtools": http://cufflinks.cbcb.umd.edu/tutorial.html

Unless it is something else, once you install "libbam.a" from samtools in the right location that error should go away.

[yueli]

Thanks GenoMax,

I have already copyed the library libbam.a and samtools in /usr/bin, make a directory called "bam" in /usr/bin, copy *.h and samtools in /usr/bin/bam.

Still got the error:

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.


Am I copy the files to the wrong direction?

Thanks in Advance for your great help!

[GenoMax]

libbam.a has to go to the "lib" directory (e.g. /usr/local/lib/).

You have not explicitly said so but is that true?

[yueli]

GenoMax,

Thank you for your answer.

I followed the manual: copyed the library libbam.a and samtools in /usr/local/lib, make a directory called "bam" in /usr/local/include, copy *.h and samtools in /usr/local/include/bam.

./configure

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.

What can I do?

Thank you so much!

[yueli]

Hi, GenoMax,

I got the right answer. I had to add --prefix= --with-bam= after ./configure.

Thank you so much!