EDGE-pro - 1.3.1

Basic information

Installation

This entry covers the entire process performed in the installation and test of EDGE-pro on a cluster with the conditions described below. It is worth mentioning that this application does not meet the Linux Directory Hierarchy Standard, so we change the directory structure to make it work with modules, Slurm, and other subsystems.

As a side note, the performance of EDGE-pro depends directly on the bowtie’s performance, so we suggest making a different tuning compilation of it.

Usage

In the following example we are going to run a test included in the source code of EDGE-pro. Note that we are using one single compute-node. Bowtie will be using OpenMP with 16 and 32 threads, in Cronos and Apolo, respectively.

Apolo

slurm_edge_pro_apolo.sh
#!/bin/bash

#SBATCH --job-name=edge_pro_test
#SBATCH --output=edge_pro_%A_%a.out
#SBATCH --error=edge_pro_%A_%a.err
#SBATCH --time=2:00
#SBATCH --partition=longjobs
#SBATCH --cpus-per-task=32

######################
# Begin work section #
######################

# Load module in default version
module load edge_pro

# Export number of threads
OMP_NUM_THREADS=32

edge.pl -g Cjejuni.fa -p Cjejuni.ptt -r Cjejuni.rnt -u wild1.fastq -s /share/apps/edge_pro/1.3.1/intel-2017_update-1/scripts -t 32

Cronos

slurm_edge_pro_cronos.sh
#!/bin/bash

#SBATCH --job-name=test_arrayjobs
#SBATCH --output=edge_pro_%A_%a.out
#SBATCH --error=edge_pro_%A_%a.err
#SBATCH --time=2:00
#SBATCH --partition=longjobs
#SBATCH --cpus-per-task=16

######################
# Begin work section #
######################

# Load module in default version
module load edge_pro

# Export number of threads
OMP_NUM_THREADS=16

edge.pl -g Cjejuni.fa -p Cjejuni.ptt -r Cjejuni.rnt -u wild1.fastq -s /share/apps/edge_pro/1.3.1/intel-18.0.2/scripts -t 16

To run the previous example.

sbatch slurm_edge_pro_[apolo|cronos].sh

Note

As you can notice in the previous examples we are using the flag -s. This is because we must specify to EDGE_pro where is the directory that contains: the built executable, the binaries of bowtie2 and additional scripts.

Note

In this example we are using the default version of EDGE-pro module. We recommend to specify the version. To use the version of this entry, pleace load the module as follow:

In Apolo II:

module load edge_pro/1.3.1_intel-2017_update-1

In Cronos:

module load edge_pro/1.3.1_intel-18.0.2

Authors