compute_optimal_binsize.pbs

#PBS -S /bin/bash
#PBS -l nodes=1:ppn=1
#PBS -l mem=2000MB
#PBS -l vmem=2000MB
#PBS -l pmem=2000MB
#PBS -l walltime=300:00:00
#PBS -q cmb
#!/bin/bash
cd "$PBS_O_WORKDIR"


binsize=$(Rscript /home/cmb-panasas2/decato/bin/compute_optimal_binsize.R ${IN};)

/home/cmb-panasas2/decato/bin/methpipe-pmd-dev/bin/pmd_rep -b ${binsize} -d ${binsize} -v -o ${IN}_${binsize}_final.pmd ${IN};