The CNVnator CNV calling tool seems to be a popular tool based on reference in papers but I am unable to get it to work. When trying to install CNVnator on a ubuntu 12.04 machine I get the error that the libcrypto.so and libssl.so.10 are missing. Googling on these libraries doesn't directly point me to a library that I should install.
I followed the README and I dowloaded the ROOT package from CERN and set the $ROOTSYS variable. I can start up the root interpreter in the ROOT package. Also I compiled the samtools tool in the CNVnator source.
When I try to build the CNVnator source I get the error below. This might be dependant on the the specific linux OS / version that I use or maybe that I didn't build the ROOT package from source. Do other people run into the same problem when installing CNVnator or does anyone know how to fix this?
The CNVnator tool (with manual in the download) is located here: http://sv.gersteinlab.org/
/src$ make
g++ -pthread -m64 -DCNVNATOR_VERSION=\"v0.2.7\" -o cnvnator obj/cnvnator.o obj/HisMaker.o obj/AliParser.o obj/Genotyper.o obj/Interval.o obj/Genome.o samtools/libbam.a -lz -L/home/William/Downloads/rootCern//lib -lCore -lCint -lRIO -lNet -lHist -lGraf -lGraf3d -lGpad -lTree -lRint -lMatrix -lPhysics -lMathCore -lThread -lGui -pthread
/usr/bin/ld: warning: libcrypto.so.10, needed by /home/William/Downloads/rootCern//lib/libNet.so, not found (try using -rpath or -rpath-link)
/usr/bin/ld: warning: libssl.so.10, needed by /home/William/Downloads/rootCern//lib/libNet.so, not found (try using -rpath or -rpath-link)
/home/William/Downloads/rootCern//lib/libNet.so: undefined reference to `EVP_sha1'
/home/William/Downloads/rootCern//lib/libNet.so: undefined reference to `SSL_CTX_new'
/home/William/Downloads/rootCern//lib/libNet.so: undefined reference to `SSL_set_fd'
/home/William/Downloads/rootCern//lib/libNet.so: undefined reference to `SSL_CTX_use_certificate_chain_file'
/home/William/Downloads/rootCern//lib/libNet.so: undefined reference to `SSL_shutdown'
/home/William/Downloads/rootCern//lib/libNet.so: undefined reference to `SSL_set_quiet_shutdown'
/home/William/Downloads/rootCern//lib/libNet.so: undefined reference to `SSL_get_error'
/home/William/Downloads/rootCern//lib/libNet.so: undefined reference to `SSL_CTX_load_verify_locations'
/home/wim/Downloads/rootCern//lib/libNet.so: undefined reference to `SSL_CTX_use_PrivateKey_file'
/home/William/Downloads/rootCern//lib/libNet.so: undefined reference to `SSLv23_method'
/home/William/Downloads/rootCern//lib/libNet.so: undefined reference to `SSL_peek'
/home/William/Downloads/rootCern//lib/libNet.so: undefined reference to `SSL_read'
/home/William/Downloads/rootCern//lib/libNet.so: undefined reference to `SSL_library_init'
/home/William/Downloads/rootCern//lib/libNet.so: undefined reference to `SSL_connect'
/home/William/Downloads/rootCern//lib/libNet.so: undefined reference to `SSL_write'
/home/William/Downloads/rootCern//lib/libNet.so: undefined reference to `SSL_free'
/home/William/Downloads/rootCern//lib/libNet.so: undefined reference to `SSL_new'
/home/William/Downloads/rootCern//lib/libNet.so: undefined reference to `HMAC'
/home/William/Downloads/rootCern//lib/libNet.so: undefined reference to `SSL_CTX_free'
collect2: ld returned 1 exit status
make: *** [cnvnator] Error 1
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written
by
William
It sounds like you are missing a couple of packages from your ubuntu installation. Try installing libssl and libcrypto:
apt-get install libssl1.0.0 libssl-dev libcrypto++9 libcrypto++-dev
You can run apt-cache to search for the libraries to find the packages if there is a mismatch between my version of ubuntu and yours.
apt-cache search libssl or apt-cache search libcrypto
Thanks, these were the libraries that I needed to install. I need to remember how to do this search and install of missing libs. To put them on the on the path so that the compilation worked I needed to symlink them to a dir on the path:
find / -name *libssl*
ln -s /lib/x86_64-linux-gnu/libssl.so.1.0.0 /usr/lib/libssl.so.10
Same for the libcrypto. And the same for the ROOT libs to run ./cnvnator (the $ROOTSYS was not enough to find the ROOT/libs/*so files )
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