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PSCBridges

PSC Receives NSF Award for Bridges Supercomputer - Read More

#!/bin/bash
#PBS -l ncpus=16
#PBS -l walltime=00:30:00
#PBS -j oe
#PBS -q batch
#PBS -N trinity_stage1
#
# Define the directory where the input data is
DATADIR=/usr/local/packages/trinity/r2012-10-05/sample_data/test_Trinity_Assembly
#
# 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 the output log
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 # # Create the directory to run the job in if it doesn't already exist mkdir -p $OUTDIR # # Move to the job directory cd $OUTDIR # # Copy input data to job directory cp $DATADIR/reads.*.fq.gz . ####################################################### ## Run Trinity to Generate Transcriptome Assemblies ## ## Stop before chrysalis ## ####################################################### 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 \ --no_run_chrysalis >& trinity_stage1_example.log ################## #### Done. #### ################## # # Copy the output files back to your home directory
cp trinity_stage1_example.log $HOME
cp trinity_stage1.output $HOME