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abyzovlab / CNVnator

a tool for CNV discovery and genotyping from depth-of-coverage by mapped reads
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Issue Installing CNVnator #154

Closed pwiner88 closed 3 years ago

pwiner88 commented 5 years ago

Hello,

I am trying to run make inside the CNVnator directory after setting a symbolic link to samtools and I get the following error:

pwiner@hpc-login3:/home/rcf-proj3/ajd/pwiner/software/CNVnator$ make Compiling with parallel (OpenMP) support g++ -O3 -std=c++11 -DCNVNATOR_VERSION=\"v0.4\" -fopenmp -I/home/rcf-proj3/ajd/pwiner/software/build/include -Isamtools -c cnvnator.cpp -o obj/cnvnator.o In file included from AliParser.hh:10:0, from cnvnator.cpp:13: samtools/sam.h:28:24: fatal error: htslib/sam.h: No such file or directory

include "htslib/sam.h"

                    ^

compilation terminated. make: *** [obj/cnvnator.o] Error 1

Any idea why? I also completed installation of root and it works fine.

suvakov commented 5 years ago

Hi, You probably did not compile samtools with htslib. Try to download latest samtools release from: https://github.com/samtools/samtools/releases After extracting files and compiling with ./configure make replace "samtools" symbolic link in your CNVnator folder with new samtools folder.