Trinity

Official website : https://github.com/trinityrnaseq/trinityrnaseq

There is no Trinity install on LANTA. We suggest using the Singularity image to bypass the installation process. For more information, please visit https://github.com/trinityrnaseq/trinityrnaseq/wiki/Trinity-in-Docker#running-trinity-using-singularity.

1 Obtaining Singularity image file
2 Job submission script

Obtaining Singularity image file

Trinity Singularity Image Archive: https://data.broadinstitute.org/Trinity/TRINITY_SINGULARITY/

for example

wget https://data.broadinstitute.org/Trinity/TRINITY_SINGULARITY/trinityrnaseq.v2.15.1.simg

Job submission script

#!/bin/bash
#SBATCH -p compute       # specific partition (compute,memory)
#SBATCH -N 1 -c 128      # -N 1 must be 1, -c can be 64, 128 depending on the requirement
#SBATCH --mem=250G       # specify required amount of RAM
#SBATCH -t 02:00:00      # job time limit <hr:min:sec>
#SBATCH -A thaisc        # project ID
#SBATCH -J Trinity       # job name

module load Apptainer/1.1.6

singularity exec -B $PWD:$PWD trinityrnaseq.v2.15.1.simg  Trinity \
                 --seqType fq \
                 --SS_lib_type RF \
                 --left data/reads_1.fq.gz  \
                 --right data/reads_2.fq.gz \
                 --max_memory 200G --CPU $SLURM_CPUS_PER_TASK \
                 --output trinity_out_dir