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Old 12-31-2013, 07:36 AM   #21
shriram
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Default CNVnator installation

This is what I have in my LD_LIBRARY_PATH
LD_LIBRARY_PATH=/compilers/gcc/4.3.5//lib:/compilers/gcc/4.3.5/lib64:${ROOTSYS}/lib
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Old 01-05-2014, 09:48 PM   #22
bhakti
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Thank you dmacmillan ! your post was very helpful .. I have installed CNVnator successfully
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Old 01-06-2014, 01:15 AM   #23
sachin
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thank you shriram..issue resolved

export PATH=/home/ionadmin/root/bin/:$PATH
export ROOTSYS=/home/ionadmin/root/
export LD_LIBRARY_PATH=/home/ionadmin/root/lib/
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Old 02-26-2015, 02:21 AM   #24
pascal
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I my case I hade to add "-lpthread" to the make file:

ROOTLIBS = -L$(ROOTSYS)/lib -ldl -lpthread -lCore -lCint -lRIO -lNet -lHist -lGraf -lGraf3d \
-lGpad -lTree -lRint -lMatrix -lPhysics \
-lMathCore -lThread -lGui
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Old 09-25-2015, 06:26 AM   #25
simobioinfo
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Hi,
I would like to install CNVnator. I installed root and setted environmental variable.
In detail, the directory where i decompressed root is /root/source-codes/root and to set environmental variable I used this code
export ROOTSYS=$HOME/root
export PATH=$PATH:$ROOTSYS/bin
export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:$ROOTSYS/lib
Then I entered into the src directory of CNVnator and typed the make command.
This is the error
g++ -m64 -DCNVNATOR_VERSION="v0.3" -I/root/root/include -Isamtools -c cnvnator.cpp -o obj/cnvnator.o
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

How don't know what is the error.
Could anyone help me?
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Old 09-26-2016, 02:59 AM   #26
cyrielle
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A Docker container for human CNV calling with CNVnator was recently developed. All you need to do is download the container and and make sure you have a WGS .bam. Calling then starts automatically, so no need to compile and run the software yourself. More info is available in this blogpost goo.gl/uodlUO.
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