Official website : https://github.com/trinityrnaseq/trinityrnaseq
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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. |
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Obtaining Singularity image file
Trinity Singularity Image Archive: https://data.broadinstitute.org/Trinity/TRINITY_SINGULARITY/
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wget https://data.broadinstitute.org/Trinity/TRINITY_SINGULARITY/trinityrnaseq.v2.15.1.simg |
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Job submission script
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###!/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 |