call_hydra.sh

 #!/bin/bash
#
# runs breakdancer against bams
#
. common.sh
export PATH=$BASE_DIR/tools/hydra-multi:$PATH
export PATH=$BASE_DIR/tools/hydra-multi/bin:$PATH
export PATH=$BASE_DIR/tools/hydra-multi/scripts:$PATH

for BAM in $DATA_DIR/*.sq.bam ; do
	cx_load $BAM
	CX_BAM=$BAM
	CX_CALLER=hydra/master20160129
	cx_save
	MAD=$(echo "scale=4; $CX_READ_FRAGMENT_STDDEV / 1.4826" | bc)
	MLD=$(echo "scale=4; 10 * $MAD" | bc)
	MNO=$(echo "scale=4; 20 * $MAD" | bc)
	# follow the hydra workflow from https://code.google.com/p/hydra-sv/wiki/TypicalWorkflow
	XC_OUTPUT=$CX.vcf
	XC_MULTICORE=1
	XC_SCRIPT="rm -rf $CX; mkdir $CX $CX 2>/dev/null; cd $CX
	module unload samtools;
	module add perl samtools/0.1.19
ulimit -n \$(ulimit -Hn)
ln -s $CX_BAM input.bam &&
echo 'sample	input.bam' > config.stub.txt &&
hydra-multi.sh run -t \$(nproc) config.stub.txt && 
$BASE_DIR/hydra2vcf.py < $CX/all.hydra.sv.final > $CX.vcf
	"
	xc_exec
done