Ray

Ray is a parallel software that computes de novo genome assemblies with next-generation sequencing data. Ray is written in C++ and can run in parallel on numerous interconnected computers using the message-passing interface (MPI) standard.

• Version: 2.3.1
• Added: August, 2014
• Max K-mer length: 32 (default at compile time)
• Default K-mer lenght: 21
• Link: http://denovoassembler.sourceforge.net/

See versions of ray which are available:

$ module avail ray

See the built-in help:

$ Ray -help | less

Running Ray on two different nodes via MPI with a total of 15 CPUs:

#!/bin/env bash
#SBATCH -p batch
#SBATCH -n 15
#SBATCH -J ray
#SBATCH --nodes=2

module load ray/2.3.1

readonly DATADIR=~/data/bfusca
readonly OUTDIR=~/data/bfusca/ray-sept26

# mpirun gets the number of processors from SLURM
mpirun Ray -k 27 -p ${DATADIR}/1_S1_L001_R1_001_val_1.fastq.gz ${DATADIR}/1_S1_L001_R2_001_val_2.fastq.gz -o ${OUTDIR}

Save in a file and submit using sbatch ray-mpi.sbatch.

Notes from the sysadmin during installation:

$ cd /tmp
$ git clone https://github.com/sebhtml/RayPlatform.git
$ git clone https://github.com/sebhtml/ray.git
$ cd ray
$ git checkout v2.3.1
$ scl enable devtoolset-1.1 bash
$ module load openmpi/1.8.2
$ make PREFIX=/export/apps/ray/2.3.1 HAVE_LIBZ=y HAVE_LIBBZ2=y
$ strip Ray
$ sudo mkdir -p /export/apps/ray/2.3.1
$ sudo chown -R aorth:aorth /export/apps/ray/2.3.1
$ make install
$ sudo chown -R root:root /export/apps/ray/2.3.1