bcbio.array.pbs

#!/bin/bash
#  runs bcbio for an array of projects listed in projects.txt
#  run with qsub -t 1-500%100 bcbio.array.pbs
#  check jobs with qstat -nt1 | grep naum
#  100 is maximum reasonable amount of running jobs in the array, cluster has 316 nodes in total

#PBS -l walltime=240:00:00,nodes=1:ppn=5
#PBS -joe .
#PBS -d .
#PBS -l vmem=50g,mem=50g

echo "START: " `date`

hostname

project=`cat projects.txt | head -n $PBS_ARRAYID | tail -n1`

cd ${project}/work

bcbio_nextgen.py ../config/${project}.yaml -n 5

echo "END: " `date`


cd ../../