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abyzovlab / CNVnator

a tool for CNV discovery and genotyping from depth-of-coverage by mapped reads
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Make error #246

Open kuangjianyu opened 3 years ago

kuangjianyu commented 3 years ago

Compiling with parallel (OpenMP) support g++ -O3 -std=c++11 -DCNVNATOR_VERSION=\"v0.4.1\" -fopenmp -I/include -Isamtools -Isamtools/htslib-1.3.1 -Isamtools/htslib-1.3.1/htslib -c cnvnator.cpp -o obj/cnvnator.o In file included from cnvnator.cpp:15: HisMaker.hh:15:10: fatal error: TFrame.h: No such file or directory 15 | #include | ^~~~~~ compilation terminated. make: *** [Makefile:70: obj/cnvnator.o] Error 1

abyzov commented 3 years ago

Hello, this error is because include files from ROOT can’t be found. Please check that you initiated ROOT environment.

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

jlchen5 commented 3 years ago

You can use conda to install it. conda create -n cnvnator_env python=3.6 conda activate cnvnator_env conda install -c conda-forge root_base=6.20 conda install -c conda-forge -c bioconda cnvnator

dridk commented 2 years ago 
conda create -n cnvnator_env python=3.6 
conda activate cnvnator_env 
conda install -c conda-forge root_base=6.20
conda install -c conda-forge -c bioconda cnvnator