Error when installing cufflinks

Question

[oma219]

Hello,

I had this error when trying to install cufflinks and it seems like a common error when I search around but I'm still not sure how to fix it. None of the methods I have found have worked for me. I installed samtools in folder and provided the path to that folder with the --with-bam option but it still says its cannot locate it?

ubuntu@ip-172-31-19-217:~/software/cufflinks-2.2.1$ ./configure --with-boost=/home/ubuntu/software/boost --with-bam=/home/ubuntu/software/samtools-1.4.1/samtools
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for gawk... gawk
checking whether make sets $(MAKE)... yes
checking for gawk... (cached) gawk
checking for g++... g++
checking for C++ compiler default output file name... a.out
checking whether the C++ compiler works... yes
checking whether we are cross compiling... no
checking for suffix of executables...
checking for suffix of object files... o
checking whether we are using the GNU C++ compiler... yes
checking whether g++ accepts -g... yes
checking for style of include used by make... GNU
checking dependency style of g++... gcc3
checking for gcc... gcc
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking dependency style of gcc... gcc3
checking whether make sets $(MAKE)... (cached) yes
checking for ranlib... ranlib
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.

[Pierre Lindenbaum]

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.

did you specify $BAM_ROOT ?

[oma219]

I tried setting $BAM_ROOT by just writing $BAM_ROOT=/home/ubuntu/software/samtools-1.4.1/ but it keeps saying its not a valid directory.

[Matteo Schiavinato]

You should probably do it with:

export BAM_ROOT=/home/ubuntu/software/samtools-1.4.1/

However, if it says that it's not a valid directory, what does it say with:

ls -l /home/ubuntu/software/samtools-1.4.1/ 
ls -l /home/ubuntu/software/samtools*

?

Answer 1

[Charles Plessy]

If your machine is running Ubuntu Vivid or later, you can just install the packaged cufflinks 2.2.1 (or ask your system administrator to do so).

For the record, here is the list of available versions as of today.

$ rmadison -uubuntu cufflinks
 cufflinks | 1.3.0-1ubuntu2 | precise/multiverse | source, amd64, armel, armhf, i386, powerpc
 cufflinks | 2.1.1-4        | trusty/multiverse  | source, amd64, arm64, armhf, i386, powerpc, ppc64el
 cufflinks | 2.2.1-1        | vivid/multiverse   | source, amd64, arm64, armhf, i386, powerpc, ppc64el
 cufflinks | 2.2.1-3        | yakkety/multiverse | source, amd64, arm64, armhf, i386, powerpc, ppc64el, s390x
 cufflinks | 2.2.1-3build1  | zesty/multiverse   | source, amd64, arm64, armhf, i386, ppc64el, s390x
 cufflinks | 2.2.1-3build1  | artful/multiverse  | source, amd64, arm64, armhf, i386, ppc64el, s390x

Answer 2

[Jeffin Rockey]

Hi,

I hope the method I have mentioned in this post for a similar problem will help.