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abyzovlab / CNVnator

a tool for CNV discovery and genotyping from depth-of-coverage by mapped reads
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Error installation #240

Open assane-mbodj opened 3 years ago

assane-mbodj commented 3 years ago

Hello

I wanted to use CNVnator and I installed all the dependencies but when I compile with make =OMP=no, I get this error message.

assane@gwas:~/CNVnator_v0.4.1/src$ make Compiling with parallel (OpenMP) support g++ -O3 -std=c++11 -DCNVNATOR_VERSION=\"v0.4.1\" -fopenmp -I/home/assane/root/include -Isamtools -c cnvnator.cpp -o obj/cnvnator.o cc1plus: error: samtools: Trop de niveaux de liens symboliques make: *** [Makefile:70 : obj/cnvnator.o] Erreur 1

Thanks for your help

abyzov commented 3 years ago

Hi, you need to have samtools directory (or link to it) from CNVnator dir. But looks like you have a file instead.

Alexej Abyzov, Ph.D. Senior Associate Consultant, Associate Professor of Biomedical Informatics, Department of Quantitative Health Sciences, Center for Individualized Medicine, Mayo Clinic

Mayo Clinic, 200 1st street SW, Harwick 3-12 Rochester, MN 55905 www.abyzovlab.orghttp://www.abyzovlab.org tel: +1-(507)-538-0978 fax: +1-(507)-284-0745