Cfm

installing cfm on server mapp

Thursday 14 October 2021

See instructions here https://bitbucket.org/wishartlab/cfm-id-code/src/master/cfm/INSTALL.md

tar -zxvf RDKit_2017_09_3.tgz cd ../.. mkdir build cd build cmake .. \ -DRDK_PGSQL_STATIC=OFF\ -DRDK_BUILD_PYTHON_WRAPPERS=OFF\ -DRDK_BUILD_CPP_TESTS=OFF\ -DRDK_BUILD_DESCRIPTORS3D=OFF\ -DRDK_INSTALL_STATIC_LIBS=OFF\ -DRDK_INSTALL_INTREE=OFF\ -DRDK_BUILD_INCHI_SUPPORT=ON\ -DRDK_OPTIMIZE_NATIVE=ON\ -DCMAKE_CXX_STANDARD=11\ -DCMAKE_BUILD_TYPE=Release make install

export LD_LIBRARY_PATH=$LD_LIBRARY_PATH::~/Programs/rdkit-Release_2017_09_3/lib:~/Programs/lp_solve_5.5/lpsolve55/bin/ux64

beware no spaces across equal sign

cmake ..
-DINCLUDE_TESTS=${BUILD_CFM_TEST}\ -DINCLUDE_TRAIN=${BUILD_CFM_TRAIN}\ -DLPSOLVE_INCLUDE_DIR=/usr/local/include/lp_solve\ -DLPSOLVE_LIBRARY_DIR=/usr/local/lib\ -DRDKIT_INCLUDE_DIR=/usr/local/include/rdkit\ -DRDKIT_INCLUDE_EXT_DIR=/usr/local/include/rdkit/External\ -DRDKIT_LIBRARY_DIR=/usr/local/lib\ -DCMAKE_CXX_STANDARD=11;\

cmake .. \ -DINCLUDE_TESTS=${BUILD_CFM_TEST}\ -DINCLUDE_TRAIN=${BUILD_CFM_TRAIN}\ -DLPSOLVE_INCLUDE_DIR=/home/allardpm/Programs/lp_solve_5.5\ -DLPSOLVE_LIBRARY_DIR=/home/allardpm/Programs/lp_solve_5.5/lpsolve55/bin/ux64\ -DRDKIT_INCLUDE_DIR=/home/allardpm/Programs/rdkit-Release_2017_09_3/Code\ -DRDKIT_INCLUDE_EXT_DIR=/home/allardpm/Programs/rdkit-Release_2017_09_3/External\ -DRDKIT_LIBRARY_DIR=/home/allardpm/Programs/rdkit-Release_2017_09_3/lib\ -DCMAKE_CXX_STANDARD=11;\

cmake .. \ -DLPSOLVE_INCLUDE_DIR=/home/allardpm/Programs/lp_solve_5.5 \ -DLPSOLVE_LIBRARY_DIR=/home/allardpm/Programs/lp_solve_5.5/lpsolve55/bin/ux64 \ -DRDKIT_INCLUDE_DIR=/home/allardpm/Programs/rdkit-Release_2017_09_3 \ -DRDKIT_INCLUDE_EXT_DIR=/home/allardpm/Programs/rdkit-Release_2017_09_3/External \ -DRDKIT_LIBRARY_DIR=/home/allardpm/Programs/rdkit-Release_2017_09_3/lib \ -DCMAKE_CXX_STANDARD=11; \

export RDBASE=~/Programs/rdkit-Release_2017_09_3/


CMake Error: The following variables are used in this project, but they are set to NOTFOUND.

Please set them or make sure they are set and tested correctly in the CMake files: INCHI_LIB (ADVANCED) linked by target "cfm-code" in directory /home/allardpm/Programs/cfm-id-code/cfm/cfm-code RDINCHI_LIB (ADVANCED) linked by target "cfm-code" in directory /home/allardpm/Programs/cfm-id-code/cfm/cfm-code

/usr/local/include/rdkit/

cmake .. \ -DINCLUDE_TESTS=${BUILD_CFM_TEST}\ -DINCLUDE_TRAIN=${BUILD_CFM_TRAIN}\ -DLPSOLVE_INCLUDE_DIR=/home/allardpm/Programs/lp_solve_5.5\ -DLPSOLVE_LIBRARY_DIR=/home/allardpm/Programs/lp_solve_5.5/lpsolve55/bin/ux64\ -DRDKIT_INCLUDE_DIR=/usr/local/include/rdkit\ -DRDKIT_INCLUDE_EXT_DIR=/usr/local/include/rdkit/External\ -DRDKIT_LIBRARY_DIR=/usr/local/lib\ -DCMAKE_CXX_STANDARD=11;\