From the ABySS web site: ABySS (Assembly By Short Sequences) is a de novo, parallel, paired-end sequence assembler that is designed for short reads. The single-processor version is useful for assembling genomes up to 100 Mbases in size. The parallel version is implemented using MPI and is capable of assembling larger genomes. We decided to document the installation of ABySS 1.2.7 First, you will need to download a dependency called " Sparsehash ". The download can be found here. Google Sparsehash Installation If you have administrative permissions then follow this section - ./configure - make - make install NB: This install the sparse hash into /usr/local/include For non administrative users - ./configure --prefix=$HOME/user - make - make install ABySS Installation Download - ./configure --prefix=/opt/exp_soft/sagrid/abyss-1.2.7 --with-mpi=/usr/lib64/openmpi CPPFLAGS=-I/opt/exp_soft/sagrid/abyss-1.2.7/google-sparsehash-1.11/include The CPPFLAGS entry is used to reference the location of the dependency installed earlier. NB: Ensure that the following is correct before continuation. The config.log file generated during the compile will indicate if the CPPFLAGS entry was successfully used. checking google/sparse_hash_map usability... yes checking google/sparse_hash_map presence... yes checking for google/sparse_hash_map... yes - make If you are running a earlier version of GCC you would see an error to the effect of " "cc1plus: warnings being treated as errors DistanceEst.cpp:392: warning: ignoring #pragma omp task " Update your make command with : - make AM_CXXFLAGS=-Wall - make install Installation is now complete and access path to the binary is available at - /opt/exp_soft/sagrid/abyss-1.2.7 - or whichever location you have made available in your --prefix=.