0.36

Installation

These are the steps to install Trimmomatic:

  1. Download the latest software version (Binaries - zip) (0.36):
cd /home/$USER/apps/trimmomatic/src
wget http://www.usadellab.org/cms/uploads/supplementary/Trimmomatic/Trimmomatic-0.36.zip
unzip Trimmomatic-0.36.zip
  1. For installation, the following steps must be done:
cd Trimmomatic-0.36
sudo mkdir -p /share/apps/trimmomatic/0.36/lib
sudo cp -r uk/ org/ net/ trimmomatic-0.36.jar /share/apps/fastqc/0.11.5/lib

Module

#%Module1.0#####################################################################
##
## module trimmomatic/0.36
##
## /share/apps/modules/trimmomatic/0.36     Written by Mateo Gomez-Zuluaga
##

proc ModulesHelp { } {
    puts stderr "\ttrimmomatic/0.36 - sets the Environment for Trimmomatic in \
    \n\tthe share directory /share/apps/trimmomatic/0.36\n"
}

module-whatis "\n\n\tSets the environment for using Trimmomatic 0.36 \
               \n\tprecompiled\n"

# for Tcl script use only
set       topdir     /share/apps/trimmomatic/0.36
set       version    0.36
set       sys        x86_64-redhat-linux

conflict trimmomatic

module load java/jdk-1.8.0_112

prepend-path CLASSPATH                      $topdir/lib/trimmomatic-0.36.jar

Mode of use

Load the necessary environment through the module:

module load trimmomatic/0.36

SLURM Template

#!/bin/sh
#SBATCH --partition=longjobs
#SBATCH --nodes=1
#SBATCH --ntasks-per-node=1
#SBATCH --time=10:00
#SBATCH --job-name=trimmomatic_example
#SBATCH -o result_%N_%j.out
#SBATCH -e result_%N_%j.err
#SBATCH --mail-type=END,FAIL
#SBATCH --mail-user=mgomezz@eafit.edu.co

# Don't share environment variables
export SBATCH_EXPORT=NONE
export OMP_NUM_THREADS=1

module load trimmomatic/0.36

java -jar /share/apps/trimmomatic/0.36/lib/trimmomatic-0.36.jar PE -phred33 input_forward.fq.gz input_reverse.fq.gz output_forward_paired.fq.gz output_forward_unpaired.fq.gz
output_reverse_paired.fq.gz output_reverse_unpaired.fq.gz ILLUMINACLIP:TruSeq3-PE.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36

TO-DO

Author

  • Mateo Gómez Zuluaga