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
#
#  Set the stack size to unlimited
ulimit -s unlimited
#
# 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
module load trinity/r2012-10-05
module load samtools/0.1.18 # # 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. #### ################## # # Copy the output files back to your home directory
cp trinity_all.log $HOME
cp trinity_all.output $HOME
Last Updated on Monday, 10 February 2014 09:54  

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