Trinity job script for all stages 

#!/bin/bash
#PBS -l ncpus=16
#PBS -l walltime=00:30:00
#PBS -j oe
#PBS -q debug
#PBS -N trinity_all
#
# Define DATADIR to be where the input files are
DATADIR=/usr/local/packages/trinity/r2012-10-05/sample_data/test_Trinity_Assembly
#
# Define OUTDIR to be the place to run the trinity job from
OUTDIR=$SCRATCH/trinity_all_example
#
# Start the accounting so details are available when trinity completes.
ja
#
# Turn echo on so all commands are echoed in the output log
set -x
#
# Set up the module command
source /usr/share/modules/init/bash
#
# Load the needed modules
# Use trinity version r2012-10-05 and java
module load trinity/r2012-10-05
module load java
#
# Create OUTDIR, which we defined above, if it does not exist already
mkdir -p $OUTDIR
#
# Move to $OUTDIR
cd $OUTDIR
#
# Copy the input data from $DATADIR to where we are, $OUTDIR
cp $DATADIR/reads.*.fq.gz .


########################################################
##  Run Trinity to Generate Transcriptome Assemblies  ##
##  Run butterfly, generate final Trinity.fasta file  ##
########################################################
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 >& trinity_all.log
##################
####   Done.  ####
##################
#
# Print the accounting report
ja -o | gawk '$3 > 10.0 {print}'
ja -set
Last Updated on Thursday, 29 November 2012 15:01  

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