#!/bin/bash -x
#
# Copyright John Reid 2009, 2010, 2011
#

#
# Set up arguments for MEME.
# See http://meme.nbcr.net/meme4_1/doc/meme.html
#

usage="USAGE: $0 <dataset> [extra optional arguments]"
dataset=${1:?$usage}
echo "Dataset=$dataset"
#DEBUG_OPTS="-print_all -trace"
DEBUG_OPTS=""
OUTPUT_DIR=output/meme
MEME=/home/john/local/bin/meme.bin
#MEME=/home/john/local/debug/bin/meme.bin
echo "MEME=$MEME"
#LD_PRELOAD=/usr/local/lib/libprofiler.so CPUPROFILE=$OUTPUT_DIR/meme.prof /home/john/local/bin/meme.bin \
$MEME \
	-dna \
	-mod anr \
	-nmotifs 1 \
	-revcomp \
	-nomatrim \
	-print_starts \
	-maxsize 1000000 \
	-oc $OUTPUT_DIR \
	$* 2>&1 | tee $OUTPUT_DIR/meme.out

