Pittsburgh Supercomputing Center 

Advancing the state-of-the-art in high-performance computing,
communications and data analytics.

#!/bin/bash
#PBS -l ncpus=16
#PBS -l walltime=00:30:00
#PBS -j oe
#PBS -q batch
#PBS -N trinity_stage4
#
# Define the directory where the job will run
OUTDIR=$SCRATCH/trinity_stage_exampl
#
#  Set the stack size to unlimited
ulimit -s unlimited
#
# Turn on echo so all commands are echoed in standard output
set -x
#
# Setup the module command
source /usr/share/modules/init/bash
#
# Load the needed modules
# Here trinity version r2014-04-13p1 is used
module load trinity/r2014-04-13p1
module load bowtie/1.0.1
module load samtools/0.1.19 # # Move to the job directory that was created in stage1 cd $OUTDIR ######################################################## ## Run Trinity to Generate Transcriptome Assemblies ## ## Run butterfly, generate final Trinity.fasta file ## ######################################################## Trinity --JM 8G --CPU 16 --bflyCPU 16 --bflyGCThreads 16 \ --seqType fq --SS_lib_type RF \ --left reads.left.fq.gz --right reads.right.fq.gz \ --output trinity_out_dir >& trinity_stage4_example.log ################## #### Done. #### ################## # # Copy the output files back to your home directory
cp trinity_stage4_example.log $HOME
cp trinity_stage4.output $HOME