CS 4884 HW

mesopelagic.sh

#!/bin/bash

#PBS -l walltime=24:00:00
#PBS -l procs=4
#PBS -q normal_q
#PBS -A cs4884s18
#PBS -W group_list=newriver

# Purge existing modules.
module purge

# Load java module for running FastViromeExplorer.
module load jdk/1.8.0

# Copy the java binaries to $WORK for fast I/O operations.
cp -r $HOME/FastViromeExplorer/bin $WORK

java -cp $WORK/bin FastViromeExplorer \
    -1 $WORK/mesopelagic/$1_1.fastq \
    -2 $WORK/mesopelagic/$1_2.fastq \
    -i $WORK/GOV_viral_contigs_EPI_MES.idx \
    -l $WORK/GOV_viral_contigs_EPI_MES_list.txt \
    -o $WORK/mesopelagic/$1