dyndna/kallisto_install_fixes.md

## kallisto_install_fixes.md

      
    Raw
  

              kallisto_install_fixes.md
            
          
    Install kallisto on HPC

cd kallisto-0.42.5/build
cmake ..

-- The C compiler identification is GNU 4.4.7
-- The CXX compiler identification is GNU 4.4.7
-- Check for working C compiler: /usr/bin/cc
-- Check for working C compiler: /usr/bin/cc -- works
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Detecting C compile features
-- Detecting C compile features - done
-- Check for working CXX compiler: /usr/bin/c++
-- Check for working CXX compiler: /usr/bin/c++ -- works
...
make

Scanning dependencies of target kallisto_core
[  5%] Building CXX object src/CMakeFiles/kallisto_core.dir/Bootstrap.cpp.o
cc1plus: error: unrecognized command line option "-std=c++11"
make[2]: *** [src/CMakeFiles/kallisto_core.dir/Bootstrap.cpp.o] Error 1
make[1]: *** [src/CMakeFiles/kallisto_core.dir/all] Error 2
make: *** [all] Error 2
Reason:


http://stackoverflow.com/a/14674646/1243763

This is because of G++ version 4.7 or less. Kallisto requires gcc >= 4.8. If you have root privileges, you can updaet G++ to recent version and problem should go away.
For HPC (cluster) machines where updated G++ may be available using module load gcc/4.8.5 command, kallisto build may fail as cmake .. seems to pick up default cc and c++ from /usr/bin and not updated c++ in user PATH.
You can export CMAKE specific enviornment variables for updated compiler as follows and do cmake .. followed by make to build kallisto.
export CC=/risapps/rhel6/gcc/4.8.5/bin/gcc
export CXX=/risapps/rhel6/gcc/4.8.5/bin/c++


http://stackoverflow.com/a/24380618/1243763

Fix

pwd


.../kallisto-0.42.5/build

# export updated compiler path to env which cmake can recognize
export CC=/risapps/rhel6/gcc/4.8.5/bin/gcc
export CXX=/risapps/rhel6/gcc/4.8.5/bin/c++

# confirm that updated compiler is present in current env
echo $CC
echo $CXX

# compile kallisto
cd .. && rm -rf build && mkdir build && cd build
cmake -DCMAKE_INSTALL_PREFIX:PATH=$HOME` ..

cmake will now recognize updated compiler

The C compiler identification is GNU 4.8.5
-- The CXX compiler identification is GNU 4.8.5
-- Check for working C compiler: /risapps/rhel6/gcc/4.8.5/bin/gcc
-- Check for working C compiler: /risapps/rhel6/gcc/4.8.5/bin/gcc -- works
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Detecting C compile features
-- Detecting C compile features - done
-- Check for working CXX compiler: /risapps/rhel6/gcc/4.8.5/bin/c++
-- Check for working CXX compiler: /risapps/rhel6/gcc/4.8.5/bin/c++ -- works
...

Build kallisto:

make
make install


kallisto binary will be at kallisto-0.42.5/build/src/kallisto and ~/bin or under path given in -DCMAKE_INSTALL_PREFIX:PATH/bin

Scanning dependencies of target kallisto_core
[  5%] Building CXX object src/CMakeFiles/kallisto_core.dir/Bootstrap.cpp.o
[ 11%] Building CXX object src/CMakeFiles/kallisto_core.dir/H5Writer.cpp.o
[ 17%] Building CXX object src/CMakeFiles/kallisto_core.dir/Kmer.cpp.o
[ 23%] Building CXX object src/CMakeFiles/kallisto_core.dir/KmerIndex.cpp.o
[ 29%] Building CXX object src/CMakeFiles/kallisto_core.dir/KmerIterator.cpp.o
[ 35%] Building CXX object src/CMakeFiles/kallisto_core.dir/MinCollector.cpp.o
[ 41%] Building CXX object src/CMakeFiles/kallisto_core.dir/PlaintextWriter.cpp.o
[ 47%] Building CXX object src/CMakeFiles/kallisto_core.dir/ProcessReads.cpp.o
[ 52%] Building CXX object src/CMakeFiles/kallisto_core.dir/PseudoBam.cpp.o
[ 58%] Building CXX object src/CMakeFiles/kallisto_core.dir/common.cpp.o
[ 64%] Building CXX object src/CMakeFiles/kallisto_core.dir/h5utils.cpp.o
[ 70%] Building CXX object src/CMakeFiles/kallisto_core.dir/hash.cpp.o
[ 76%] Building CXX object src/CMakeFiles/kallisto_core.dir/main.cpp.o
[ 82%] Building CXX object src/CMakeFiles/kallisto_core.dir/weights.cpp.o
[ 88%] Linking CXX static library libkallisto_core.a
[ 88%] Built target kallisto_core
Scanning dependencies of target kallisto
[ 94%] Building CXX object src/CMakeFiles/kallisto.dir/main.cpp.o
[100%] Linking CXX executable kallisto
[100%] Built target kallisto
If you get error, GLIBCXX_3.*.* not found while running kallisto, it is likely because of incorrect version of libstdc++.so.6 library sourced in user environment. Check LD_LIBRARY_PATH and make sure that it being sourced from updated gcc, e.g., /risapps/rhel6/gcc/4.8.5/lib64/libstdc++.so.6 and not /lib64/ or /usr/lib64/.
END