0.36¶
- Installation date: 01/03/2017
- URL: http://www.usadellab.org/cms/?page=trimmomatic
- Apolo version: Apolo II
- License: GNU GENERAL PUBLIC LICENSE, Version 3
Tabe of Contents
Installation¶
These are the steps to install Trimmomatic:
- 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
- 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