Trinity is available on the high memory nodes.

To load Trinity type the following:

$ module load bigmem trinity

Check to see if your stack size is unlimited:

$ ulimit -s
unlimited

To run submit a batch job running trinity with 8 CPUs create a file with:

#!/bin/bash
#$ -cwd
#$ -S /bin/bash
#$ -pe threaded 8

module load bigmem trinity

Trinity.pl --seqType fq --left end_trim_5_1.fastq --right end_trim_5_3.fastq --CPU 8 --kmer_method inchworm

Then to submit it to the queue, cd into the directory with the input files:

cd ~/Project1/Run12
qsub <filename of script>