RAY

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Ray: Parallel genome assemblies for parallel DNA sequencing
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.
Manual

Module: Example

[]$ [salexan5@tlog2 Ray]$ module spider ray

  ray: ray/2.3.1

    This module can be loaded directly: module load ray/2.3.1

    Help:
      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.
      
      see: http://denovoassembler.sourceforge.net/index.html
module load ray/2.3.1

Using:

Testing: Based on User Manual
Example 1: Using one node, with ten tasks (one core per task). Notice that the srun -n option is set to 1 * 10 = 10:

#!/bin/bash
#SBATCH --account=type-your-project-name
#SBATCH --time=00:30:00
#SBATCH --nodes=1
#SBATCH --ntasks-per-node=10
#SBATCH --cpus-per-task=1
#SBATCH --output=ray_%A.out

module load ray/2.3.1

srun -n 10 Ray -o test -p test_file_1.fastq test_file_2.fastq -k 31

Example 2: Using five nodes, with sixteen tasks per node (one core per task). Notice that the srun -n option is set to 5 * 16 = 80:

#!/bin/bash
#SBATCH --account=type-your-project-name
#SBATCH --time=00:10:00
#SBATCH --nodes=5
#SBATCH --ntasks-per-node=16
#SBATCH --cpus-per-task=1
#SBATCH --output=ray_%A.out

module load ray/2.3.1

srun -n 80 Ray -o test -p test_file_1.fastq test_file_2.fastq -k 31


  • This software is dependent on the following modules:
    • swset/2018.05
    • gcc/7.3.0
    • intel-mpi/2018.2.199
    • The module load ray/2.3.1 line will automatically load these modules for you.


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