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=.