#!/bin/bash
#
###############################################################################
#
# "run_deconseq.sh" SuperMikeII script 
# created by Jean P. Elbers
# jean.elbers@gmail.com
# last edited 5 December 2014
#
###############################################################################
#
#PBS -q workq
#PBS -A hpc_startup_albuseb
#PBS -l nodes=1:ppn=16
#PBS -l walltime=04:00:00
#PBS -o /work/albuseb/deconseq_out/
#PBS -j oe
#PBS -N run_deconseq.sh

# Let's mark the time things get started with a date-time stamp.

date

# Set work directory

export WORK_DIR=/home/albuseb/bin/deconseq-standalone-0.4.3

# Makes BWA index for the 4 deconseq_ref.fa_c#.fasta files

cd $WORK_DIR
perl /home/albuseb/bin/deconseq-standalone-0.4.3/deconseq_16cores.pl \
-f /work/albuseb/folder_containing_fastq_or_fasta_to_filter/file_to_filter.fastq \
-dbs deconseq_ref \
-out_dir /work/albuseb/deconseq_out