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abyzovlab / CNVnator

a tool for CNV discovery and genotyping from depth-of-coverage by mapped reads
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Can not install CNVnator #152

Closed tongshiyuan closed 3 years ago

tongshiyuan commented 5 years ago

Hi， I use the cmd line as follow： $ git clone https://github.com/abyzovlab/CNVnator.git $ cd CNVnator $ ln -s /biosoft/samtools-1.9/ samtools $ mkdir yeppp && cd yeppp $ wget http://bitbucket.org/MDukhan/yeppp/downloads/yeppp-1.0.0.tar.bz2 $ tar xjf yeppp-1.0.0.tar.bz2 $ make YEPPPLIBDIR=/biosoft/CNVnator/yeppp/yeppp-1.0.0/binaries/linux/x86_64/ YEPPPINCLUDEDIR=/biosoft/CNVnator/yeppp/yeppp-1.0.0/library/headers

and install error：

Compiling with parallel (OpenMP) support g++ -O3 -std=c++11 -DCNVNATOR_VERSION=\"v0.4\" -fopenmp -o cnvnator obj/cnvnator.o obj/EXOnator.o obj/HisMaker.o obj/AliParser.o obj/FastaParser.o obj/VcfParser.o obj/Genotyper.o obj/Interval.o obj/Genome.o samtools/libbam.a samtools/htslib-1.9/libhts.a -lz -lbz2 -lcurl -llzma -L/biosoft/CNVnator/yeppp/yeppp-1.0.0/binaries/linux/x86_64/ -lyeppp -L/biosoft/root/build/lib -lCore -lRIO -lHist -lGraf -lGpad -lTree -lMathCore /usr/bin/ld: samtools/htslib-1.9/libhts.a(hfile_s3.o): undefined reference to symbol 'HMAC@@OPENSSL_1_1_0' //usr/lib/x86_64-linux-gnu/libcrypto.so.1.1: error adding symbols: DSO missing from command line collect2: error: ld returned 1 exit status Makefile:63: recipe for target 'cnvnator' failed make: *** [cnvnator] Error 1

What can we do to solve this? And what version of samtools is required?

suvakov commented 5 years ago

Can you please try to compile with: make clean make LIBS="-lcrypto"

tongshiyuan commented 5 years ago

Can you please try to compile with: make clean make LIBS="-lcrypto"

Thanks， And when I do that, install maybe done with no error. But when I run cnvnator, report an error

./cnvnator: error while loading shared libraries: libCore.so: cannot open shared object file: No such file or directory

abyzov commented 5 years ago

Hi, looks like you don’t have set a proper environment for ROOT libs. You may need to do . /path_to_root/bin/thisroot.sh

Alexej Abyzov, Ph.D. Senior Associate Consultant, Assistant Professor of Biomedical Informatics, Department of Health Sciences Research, 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

On May 13, 2019, at 8:28 PM, tongshiyuan notifications@github.com<mailto:notifications@github.com> wrote:

Can you please try to compile with: make clean make LIBS="-lcrypto"

Thanks， And when I do that, install maybe done with no error. But when I run cnvnator, report an error

./cnvnator: error while loading shared libraries: libCore.so: cannot open shared object file: No such file or directory

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