How to install tophat in Debian?
Vra
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?
Oplossing
SAMtools must be proparly packaged, otherwise TopHat cannot use them. So:
- Build BAM from the source first. Get it at http://samtools.sourceforge.net/.
- Choose the BAM installation folder (I refer it as install below).
- Copy all C header files to install/include/bam.
- Copy libbam.a to install/lib.
- Place samtools binary on your path.
- For TopHat, try ./configure --with-bam=install
- If this does not work for some strange reason, try also export BAM_ROOT=install before running ./configure.
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