CNVnator installation error

Question

[xiaoyonf]

Hi, I tried to install the CNVnator in MAC v10.10.5 terminal. I followed the procedures by searching online instruction in ROOTSYS setup. I have the final step showing the error message as below,

xiaoyongs-mbp:src MyBioinformatics$ make
g++ -m64 -DCNVNATOR_VERSION=\"v0.3\" -I/include -Isamtools -c cnvnator.cpp -o obj/cnvnator.o
In file included from cnvnator.cpp:8:
./HisMaker.hh:11:10: ****fatal error: ****'TFrame.h' file not found
#include <TFrame.h>
         ^
1 error generated.
make: *** [obj/cnvnator.o] Error 1

Does anyone have the same experience when installing the CNVnator? What is the TFrame.h file and how to fix it?

Thank you very much!

[Leandro Lima]

Hi xiaoyonf.

If you install speedseq, you can get CNVnator installed very easily.

Leandro

Answer 1

[donfreed]

The compiler can not find all of the files it needs to compile CNVnator because your environment is not correctly set. Specifically, you need to set the LD_LIBRARY_PATH and ROOTSYS variables.

See these links for additional help:

• http://seqanswers.com/forums/showthread.php?t=16665
• https://github.com/hall-lab/speedseq#cnvnator

[sukesh1411]

Hi

I followed the above links and installed root but could not install CNVnator. I tried but i am end up with follow error..

In file included from cnvnator.cpp:8:0:
HisMaker.hh:11:20: fatal error: TFrame.h: No such file or directory
 #include <TFrame.h>
                    ^
compilation terminated.
make: *** [obj/cnvnator.o] Error 1

I think am doing mistake somewhere while setting the path.

export ROOTSYS=/usr/include/root/
export LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${ROOTSYS}/lib.. please help me to install CNVnator