ray-software
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Table of Contents
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.
Information
- Version: 2.3.1
- Added: August, 2014
- Max K-mer length: 32 (default at compile time)
- Default K-mer lenght: 21
Usage
See versions of ray which are available
module avail ray
See the built-in help
Ray -help | less
Example batch job
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
.
Installation
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
ray-software.1411740064.txt.gz · Last modified: 2014/09/26 14:01 by aorth