Thursday, April 25, 2013

Unable to detect bamlib libraries (version or higher) when installing cufflinks

If you are installing Cufflinks according to the instructions as given by 

The compiling of the components below are quite expected.

But when finally compiling cufflinks, you might encounter errors
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......... 
See for more documentation. 
The source of the error is somehow the cufflinks is not able to find the libraires and binaries found by samtools. This is especially true if you compiled the components into distinct directories and not into standard directories like /usr/local/bin and /usr/local/lib /usr/local/include

To ensure that the cufflinks detects the samtools libraries, you might want to do the following.
# mkdir -p /usr/local/include/bam
# cp ${SAMTOOLS}/libbam.a /usr/local/lib/
# cp ${SAMTOOLS}/*.h /usr/local/include/bam
# cp ${SAMTOOLS}/samtools /usr/local/bin/

Try compiling again. It should work


Ivarz said...

Thanks, worked like a charm

Danilo da Silva said...

What if I have these somewhere else? I'm trying --with-bam with no luck :(

J. Marcelo Alves said...

Did all that is listed here (latest cufflinks from GitHub), still getting the error about not being able to find bamlib... This problem seems to be at least 5 years old, from my searches on line (wrong URL still being listed by ./configure, for example), and people are still having problems with this. Pathetic.

By the way, I tried both of these (even if ./cofigure tells me not to):
export BAM_ROOT=/usr/local/include/bam/

Unknown said...

I think I solved the issue.
In additional to the mentioned 4 steps, we also need to rename XXX/include/bam/version.h to XXX/include/bam/version.hpp. This is of course a bug.

Unknown said...

Thanks! This solved it! Note that make install under samtools does NOT put things in the places expected by cuffdiff configure.

Lucas said...

Thanks Xingyu Yang, it solved my issue too!

Lucas said...

Thanks Xingyu Yang, it solved my issue too!

Ty said...

Thanks Xingyu Yang!

tek said...

Xingyu Yang said that it is run for me, thanks a lot.

tek said...

It is Xingyu Yang said that it is run for me, thanks a lot.

Unknown said...

That's iNDEED a HUGE BUG!! thank you Xingyu Yang!!! Really saved me from keep ./configure