#!/bin/bash
#$ -S /bin/bash
#$ -N giab-1
#$ -q mpi.q
#$ -pe openmpi 48
#$ -l mem_token=11G,mem_free=11G,h_vmem=11G,excl=true
#$ -j y
#$ -o log/$JOB_NAME.$JOB_ID.$TASK_ID
#$ -m ae
#$ -M sjackman@gmail.com

#------------------------------------------------------------
# job params
#------------------------------------------------------------

export k=$SGE_TASK_ID
export name=hsapiens
export lib=pe600
export pe600=`<pe600.in`
export mp=mp6k
export mp6k=`<mp6k.in`

#------------------------------------------------------------
# run the assembly
#------------------------------------------------------------

# only run the preunitigs stage
export stages=preunitigs

source /extscratch/btl/bloom-dbg/assembler-comparison/common/run-abyss-1.9.0-genesis \
	   mplib_de='--mean' "$@"
