How to install tophat in Debian?

Question

I have tried searching and trying everything. I have bowtie, samtools and libbam-dev installed in my system. While running ./configure I am getting this 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.

How do I solve this error and install tophat?

Answer 1

SAMtools must be proparly packaged, otherwise TopHat cannot use them. So:

1. Build BAM from the source first. Get it at http://samtools.sourceforge.net/.
2. Choose the BAM installation folder (I refer it as install below).
3. Copy all C header files to install/include/bam.
4. Copy libbam.a to install/lib.
5. Place samtools binary on your path.
6. For TopHat, try ./configure --with-bam=install
7. If this does not work for some strange reason, try also export BAM_ROOT=install before running ./configure.