Arkansas High Performace Computing Center [hpcwiki]

Trinity combines three independent software modules: Inchworm, Chrysalis, and Butterfly, applied sequentially to process large volumes of RNA-seq reads. Trinity was developed at the Broad Institute and the Hebrew University of Jerusalem. You can find more information on Trinity here.

Edit your $HOME/.bashrc file to contain the line of code below which will include the dependency for Trinity. You will have to log back in for this to take effect.

module load trinity/2.3.2

In your $HOME directory create a directory called TRINITY-JOBS to store the files we will be using. Copy the testing files created be Trinity into the new directory.

razor-l1:jokinsey:~$ mkdir TRINITY-JOBS
razor-l1:jokinsey:~$ cp /share/apps/trinity/trinityrnaseq-2.3.2/sample_data/test_Trinity_Assembly/reads.left.fq.gz ./TRINITY-JOBS/
razor-l1:jokinsey:~$ cp /share/apps/trinity/trinityrnaseq-2.3.2/sample_data/test_Trinity_Assembly/reads.right.fq.gz ./TRINITY-JOBS/

Now inside the new directory create a PBS script named trinity.pbs to run the job, that contains the information below.

#!/bin/bash
#PBS -N trinity
#PBS -q tiny12core
#PBS -j oe
#PBS -o trinity.$PBS_JOBID
#PBS -l nodes=1:ppn=12
#PBS -l walltime=1:00:00

cd $PBS_O_WORKDIR
mkdir trinity.$PBS_JOBID
cp reads.right.fq reads.left.fq /scratch/$PBS_JOBID
cd /scratch/$PBS_JOBID

Trinity --seqType fq --left reads.left.fq --right reads.right.fq --CPU $PBS_NUM_PPN --max_memory 8G --output $PBS_O_WORKDIR/trinity.$PBS_JOBID

All thats left is to submit the job.

razor-l1:jokinsey:~/TRINITY-JOBS$ qsub trinity.pbs

The output of this job will be located in a new directory trinity.$PBS_JOBID created where the job is run from. There will be a lot of files in this output directory, and a good starting file to look at is the Trinity.fasta file. More information on the output is located here.