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_stage2
#
# Define the directory where the job will run
OUTDIR=$SCRATCH/trinity_stage_example
#
#  Set the stack size to unlimited
ulimit -s unlimited
#
# Turn echo on so all commands are echoed in standard output
set -x
#
# Setup the module command
source /usr/share/modules/init/bash
#
# Load the needed module
# Here trinity version r2012-10-05 is used
module load trinity/r2012-10-05
#
# Move to the job directory that was created in stage1
cd $OUTDIR
##################################################################
##  Run Trinity to Generate Transcriptome Assemblies            ##
##  Chrysalis clustering of inchworm contigs and mapping reads  ##
##################################################################
Trinity.pl --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 \
--no_run_quantifygraph >& trinity_stage2_example.log
##################
####   Done.  ####
##################
#
# Copy the output files back to your home directoy
cp trinity_stage2_example.log $HOME cp trinity_stage2.output $HOME

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