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 -o runtrinity.out
#PBS -q debug
#PBS -N runtrinity
# define where the input data is stored
DATADIR=~nigra/trinity/data
# turn on accounting
ja
# turn on echo
set -x
# set up the module command
source /usr/share/modules/init/bash
# load the trinity module
# Here we use version r2012-05-18
# Be careful to load the specific version you want
module load trinity/r2012-05-18
# move to your scratch directory
cd $SCRATCH
# copy the input data here
cp $DATADIR/reads.*.fq.gz .
#######################################################
##  Run Trinity to Generate Transcriptome Assemblies ##
##                                                   ##
##  redirect trinity output to a file in $SCRATCH    ##
##                                                   ##
##  IMPORTANT NOTE                                   ##
##  So that you can see the                          ##
##  entire trinity command line on your screen       ##
##  we've broken it up here into multiple lines.     ##
##  When you submit a job, BE SURE  that             ##
##  your trinity command is all on one line.         ##
#######################################################
Trinity.pl --seqType fq --kmer_method jellyfish --max_memory 8G --left reads.left.fq.gz 
     --right reads.right.fq.gz --SS_lib_type RF --group_pairs_distance 501 
     --path_reinforcement_distance 76 --min_contig_length 201 --CPU 12 --bflyCPU 12 
     --bflyGCThreads 12 --bfly_opts "-V10 --stderr" > trinity.output
#############################
####   Done.  ###############
#############################
cp -r trinity_out_dir $DATADIR
cp trinity.output $DATADIR
# get some job statistics
ja -o | gawk '$3 > 10.0 {print}'
ja -set

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