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Published 20 hours ago • verified publisher icon cole-trapnell-lab

cannot install cufflinks 2.2.1 from source due to bamlib error

Open ashwinkelkar opened this issue 8 years ago • 4 comments

I am using Ubuntu 15.04 for installing cufflinks 2.2.1 from source. I have installed samtools as per the instruction manual steps: All the files are in their correct locations (/usr/local/bin for the binaries /usr/local/include/bam for the headers and /usr/local/lib for the libbam.a and the libhts.a )

Now whenever I try doing a ./configure I get the following 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.

I am running samtools as a GLOBAL installtion. it works from the terminal as it is because it is in the default $PATH. Thus now when I do a global installation for cufflinks it should find the files in the right location. But this does not seem to happen I also tried installing an earlier version of samtools 0.19.0 but the error persists. Any tips would be appreciated.

ashwinkelkar avatar May 31 '16 10:05 ashwinkelkar

I have the same problem, and couldn;t work it out.

crystalpang avatar Sep 02 '16 02:09 crystalpang

I am also having same problem tried to trouble shoot from here but didn't work for me. https://groups.google.com/forum/#!topic/tuxedo-tools-users/LCysdlmkEgk

beetlejuice007 avatar Feb 05 '18 07:02 beetlejuice007

Hello,

I have exactly the same problem. The tips given in the google group didn't work for me either.

rmontagn avatar Feb 12 '18 16:02 rmontagn

cannot install cufflinks 2.2.1 from source due to bamlib error

I have same error when trying to run ./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.

Please Help

rachko1 avatar Dec 01 '18 07:12 rachko1